Sandwiched graphene--membrane superstructures

A Review on Investigating the Interactions between Nanoparticles and the Pulmonary Surfactant Monolayer with Coarse-Grained Molecular Dynamics Method

Pulmonary drug delivery has garnered significant attention due to its targeted local lung action, minimal toxic side effects, and high drug utilization. However, the physicochemical properties of inhaled nanoparticles (NPs) used as drug carriers can influence their interactions with the pulmonary surfactant (PS) monolayer, potentially altering the fate of the NPs and impairing the biophysical function of the PS monolayer. Thus, the objective of this review is to summarize how the physicochemical properties of NPs affect their interactions with the PS monolayer. Initially, the definition and properties of NPs, as well as the composition and characteristics of the PS monolayer, are introduced. Subsequently, the coarse-grained molecular dynamics (CGMD) simulation method for studying the interactions between NPs and the PS monolayer is presented. Finally, the implications of the hydrophobicity, size, shape, surface charge, surface modification, and aggregation of NPs on their interactions with the PS monolayer and on the composition of biomolecular corona are discussed. In conclusion, gaining a deeper understanding of the effects of the physicochemical properties of NPs on their interactions with the PS monolayer will contribute to the development of safer and more effective nanomedicines for pulmonary drug delivery.

Cholesterols Induced Distinctive Entry of the Graphene Nanosheet into the Cell Membrane

Graphene nanosheets are highly valued in the biomedical field due to their potential applications in drug delivery, biological imaging, and biosensors. Their biological effects on mammalian cells may be influenced by cholesterols, which are crucial components in cell membranes that take part in many vital processes. Therefore, it is particularly important to investigate the effect of cholesterols on the transport mechanism of graphene nanosheets in the cell membrane as well as the final stable configuration of graphene, which may have an impact on cytotoxicity. In this paper, the molecular details of a graphene nanosheet interacting with a 1,2-dipalmitoyl-sn-glycero-3-phosphorylcholine (DPPC) membrane with cholesterols were studied using molecular dynamics simulations. Results showed that the structure of the graphene nanosheet transits from the cut-in state in a pure DPPC membrane to being sandwiched between two DPPC leaflets when cholesterols reach a certain concentration. The underlying mechanism showed that cholesterols are preferentially adsorbed on the graphene nanosheet, which causes a larger disturbance to the nearby DPPC tails and thus guides the graphene nanosheet into the core of lipid bilayers to form a sandwiched structure. Our results are helpful for understanding the fundamental interaction mechanism between the graphene nanosheet and cell membrane and to explore the potential applications of the graphene nanosheet in biomedical sciences.

Synthesis of Zwitterionic Phospholipid-Connected Silane Coupling Agents and Their Hybridization with Graphene Oxide

The hybridization of lipids with graphene is expected to produce a promising, novel biomaterial. However, there are limited examples of the covalent introduction of lipid molecules, especially the immobilization of lipid molecules, onto graphene on a substrate. Therefore, we investigated the hybridization of a silane coupling agent having phospholipid moieties with graphene oxide on substrates prepared by photo-oxidation using chlorine dioxide. Three silane coupling agents with different carbon chain lengths (C4, C6, C8) were synthesized and phospholipid molecules were introduced onto graphene on a substrate. Phospholipid-immobilized graphene on a grid for TEM (transmission electron microscope) was used for EM analysis of proteins (glyceraldehyde 3-phosphate dehydrogenase and β-galactosidase), enabling the observation of sufficient particles compared to the conventional graphene grid.

Graphene-Based Nanomaterials and Their Interactions with Lipid Membranes

Graphene-based nanomaterials (GNMs) have captured increasing attention in the recent advancement of materials science and nanotechnology owing to their excellent physicochemical properties. Despite having unquestionable advances, the application of GNMs in biological and medical sciences is still limited due to the lack of knowledge and precise control over their interaction with the biological milieu. The cellular membrane is the first barrier with which GNMs interact before entering a cell. Therefore, understanding how they interact with cell membranes is important from the perspective of safe use in biological and biomedical fields. In this review, we systematically summarize the recent efforts in predicting the interactions between GNMs and model cellular membranes. This review provides insights into how GNMs interact with lipid membranes and self-assemble in and around them. Both the computational simulations and experimental observations are summarized. The interactions are classified depending on the physicochemical properties (structure, chemistry, and orientation) of GNMs and various model membranes. The thermodynamic parameters, structural details, and supramolecular forces are listed to understand the interactions which would help circumvent potential risks and provide guidance for safe use in the future. At the end of this review, future prospective and emerging challenges in this research field are discussed.

Pure Graphene Acts as an "Entropic Surfactant" at the Octanol-Water Interface

Graphene oxide (GO) has proved itself as a nanomaterial capable of acting as a surfactant by lowering the interfacial tension of the oil-water interface due to its polar oxygen groups. However, the surfactant behavior of the pure graphene sheet─since prevention of edge oxidation in experimental setups is nontrivial─is still an unresolved issue in graphene research despite significant progress in the field in recent years. Here, we conduct both atomistic and coarse-grained simulations to demonstrate that─surprisingly─even pristine graphene, which only consists of hydrophobic carbon atoms, is attracted to the octanol-water interface and consequently reduces its surface tension by 2.3 kBT/nm2 or about 10 mN/m. Interestingly, the location of the free energy minimum is not precisely at the oil-water interface itself but is rather buried about two octanol layers into the octanol phase, being about 0.9 nm from the water phase. We demonstrate that the observed surfactant behavior is purely entropically driven and can be attributed to the unfavorable lipid-like structuring of octanol molecules at the free octanol-water interface. In essence, graphene enhances the inherent lipid-like behavior of octanol at the water interface rather than directly acting as a surfactant. Importantly, graphene does not display surfactant-like behavior in corresponding Martini coarse-grained simulations of the octanol-water system since the free liquid-liquid interface loses essential structure at the lower coarse-grained resolution. However, a similar surfactant behavior is recovered in coarse-grained simulations of longer alcohols such as dodecan-1-ol and hexadecan-1-ol. The observed discrepancies at different model resolutions enable us to construct a comprehensive model of the surfactant behavior of graphene at the octanol-water interface. The here-gained insights may facilitate the broader utilization of graphene in numerous domains of nanotechnology. Furthermore, since a drug's octanol-water partition coefficient is a crucial physicochemical parameter in rational drug discovery, we also believe that the universality of the here-illustrated entropic surfactant behavior of planar molecules deserves special attention in the drug design and development field.

Mesoscale computer modeling of asphaltene aggregation in liquid paraffin

Asphaltenes represent a novel class of carbon nanofillers that are of potential interest for many applications, including polymer nanocomposites, solar cells, and domestic heat storage devices. In this work, we developed a realistic coarse-grained Martini model that was refined against the thermodynamic data extracted from atomistic simulations. This allowed us to explore the aggregation behavior of thousands of asphaltene molecules in liquid paraffin on a microsecond time scale. Our computational findings show that native asphaltenes with aliphatic side groups form small clusters that are uniformly distributed in paraffin. The chemical modification of asphaltenes via cutting off their aliphatic periphery changes their aggregation behavior: modified asphaltenes form extended stacks whose size increases with asphaltene concentration. At a certain large concentration (44 mol. %), the stacks of modified asphaltenes partly overlap, leading to the formation of large, disordered super-aggregates. Importantly, the size of such super-aggregates increases with the simulation box due to phase separation in the paraffin-asphaltene system. The mobility of native asphaltenes is systematically lower than that of their modified counterparts since the aliphatic side groups mix with paraffin chains, slowing down the diffusion of native asphaltenes. We also show that diffusion coefficients of asphaltenes are not very sensitive to the system size: enlarging the simulation box results in some increase in diffusion coefficients, with the effect being less pronounced at high asphaltene concentrations. Overall, our findings provide valuable insight into the aggregation behavior of asphaltenes on spatial and time scales that are normally beyond the scales accessible for atomistic simulations.

Graphene Oxide Hosting a pH-Sensitive Prodrug: An In Silico Investigation of Graphene Oxide-Based Nanovehicle toward Cancer Therapy

Prodrug and drug delivery systems are two effective strategies for improving the selectivity of chemotherapeutics. Herein, via molecular dynamics (MD) simulation and free energy calculation, the effectiveness of the graphene oxide (GO) decorated with the pH-sensitive prodrug (PD) molecules in cancer therapy is investigated. PEI-CA-DOX (prodrug) was loaded onto the GO surface, in which the hydrogen bonding and pi-pi stacking interactions play the main role in the stability of the GO-PD complex. Due to the strong interaction of GO and PD (about -800 kJ/mol), the GO-PD complex remains stable during the membrane penetration process. The obtained results confirm that GO is a suitable surface for hosting the prodrug and passing it through the membrane. Furthermore, the investigation of the release process shows that the PD can be released under acidic conditions. This phenomenon is due to the reduction of the contribution of electrostatic energy in the GO and PD interaction and the entry of water into the drug delivery system. Moreover, it is found that an external electrical field does not have much effect on drug release. Our results provide a deep understanding of the prodrug delivery systems, which helps the combination of nanocarriers and modified chemotherapy drugs in the future.

Converting Nanotoxicity Data to Information Using Artificial Intelligence and Simulation

Decades of nanotoxicology research have generated extensive and diverse data sets. However, data is not equal to information. The question is how to extract critical information buried in vast data streams. Here we show that artificial intelligence (AI) and molecular simulation play key roles in transforming nanotoxicity data into critical information, i.e., constructing the quantitative nanostructure (physicochemical properties)-toxicity relationships, and elucidating the toxicity-related molecular mechanisms. For AI and molecular simulation to realize their full impacts in this mission, several obstacles must be overcome. These include the paucity of high-quality nanomaterials (NMs) and standardized nanotoxicity data, the lack of model-friendly databases, the scarcity of specific and universal nanodescriptors, and the inability to simulate NMs at realistic spatial and temporal scales. This review provides a comprehensive and representative, but not exhaustive, summary of the current capability gaps and tools required to fill these formidable gaps. Specifically, we discuss the applications of AI and molecular simulation, which can address the large-scale data challenge for nanotoxicology research. The need for model-friendly nanotoxicity databases, powerful nanodescriptors, new modeling approaches, molecular mechanism analysis, and design of the next-generation NMs are also critically discussed. Finally, we provide a perspective on future trends and challenges.

Recent advances and mechanism of antimicrobial efficacy of graphene-based materials: a review

Graphene-based materials have undergone substantial investigation in recent years owing to their wide array of physicochemical characteristics. Employment of these materials in the current state, where infectious illnesses caused by microbes have severely damaged human life, has found widespread application in combating fatal infectious diseases. These materials interact with the physicochemical characteristics of the microbial cell and alter or damage them. The current review is dedicated to molecular mechanisms underlying the antimicrobial property of graphene-based materials. Various physical and chemical mechanisms leading to cell membrane stress, mechanical wrapping, photo-thermal ablation as well as oxidative stress exerting antimicrobial effect have also been thoroughly discussed. Furthermore, an overview of the interactions of these materials with membrane lipids, proteins, and nucleic acids has been provided. A thorough understanding of discussed mechanisms and interactions is essential to develop extremely effective antimicrobial nanomaterial for application as an antimicrobial agent.

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Damage Effect of Amorphous Carbon Black Nanoparticle Aggregates on Model Phospholipid Membranes: Surface Charge, Exposure Concentration and Time Dependence

Commercial nano-scale carbon blacks (CB) are being harnessed widely and may impose potentially hazardous effects because of their unique properties, especially if they have been modified to grow reactive functional groups on their surface. Cytotoxicity of CB has been well studied but the membrane damage mechanisms and role of surface modification are still open to debate. Negatively and positively charged giant unilamellar vesicles (GUVs) were prepared using three lipids as model cell membranes to examine the mechanistic damage of CB and MCB (modified by acidic potassium permanganate) aggregates. Optical images showed that both anionic CB and MCB disrupted the positively charged but not the negatively charged GUVs. This disruption deteriorated with the rise and extension of exposure concentration and time. Lipids extraction caused by CBNs (CB and MCB together are called CBNs) was found. MCB caused more severe disruption than CB. MCB was enveloped into vesicles through an endocytosis-like process at 120 mg/L. MCB mediated the gelation of GUVs, perhaps through C-O-P bonding bridges. The lower hydrodynamic diameter and more negative charges may have been responsible for the distinction effect of MCB over CB. The adhesion and bonding of CBNs to the membrane were favored by electrostatic interaction and the practical application of CBNs warrants more attention.

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.

Mass Spectrometry and Cryogenic Electron Microscopy Illuminate Molecular-Level Mechanisms of the Oxidative and Structural Damage to Lipid Membranes by Radical-Bearing Graphene Oxide

Biomedical applications of graphene in tumor and bacterial treatment have become cutting-edge fields due to its unique physical and chemical properties. However, a mechanistic understanding of the interactions and reactions between graphene-based material and biological systems such as lipid membranes remains elusive, especially at the molecular level. By using the unique field-induced droplet ionization mass spectrometry and cryogenic electron microscopy methodologies, we reveal the oxidation products of monolayer lipid membranes at the air-water interface and the change in the morphology of bilayer lipid membranes in an aqueous solution caused by the incorporation of graphene oxide bearing π-conjugated carbon radicals [hydrated graphene oxide (hGO)]. We discovered that hGO is an efficient source of hydroxyl radicals and that it is not only the incorporation of the hGO sheets but also the irregular packing of the lipid oxides from the hydroxyl radical oxidation that causes the structural distortions of the liposomes.

Coarse-grained molecular models of the surface of hair

We present a coarse-grained molecular model of the surface of human hair, which consists of a supported lipid monolayer, in the MARTINI framework. Using coarse-grained molecular dynamics (MD) simulations, we identify a lipid grafting distance that yields a monolayer thickness consistent with both atomistic MD simulations and experimental measurements of the hair surface. Coarse-grained models for fully-functionalised, partially damaged, and fully damaged hair surfaces are created by randomly replacing neutral thioesters with anionic sulfonate groups. This mimics the progressive removal of fatty acids from the hair surface by bleaching and leads to chemically heterogeneous surfaces. Using molecular dynamics (MD) simulations, we study the island structures formed by the lipid monolayers at different degrees of damage in vacuum and in the presence of polar (water) and non-polar (n-hexadecane) solvents. We also use MD simulations to compare the wetting behaviour of water and n-hexadecane droplets on the model surfaces through contact angle measurements, which are compared to experiments using virgin and bleached hair. The model surfaces capture the experimentally-observed transition of the hair surface from hydrophobic (and oleophilic) to hydrophilic (and oleophobic) as the level of bleaching damage increases. By selecting surfaces with specific damage ratios, we obtain contact angles from the MD simulations that are in good agreement with experiments for both solvents on virgin and bleached human hairs. To negate the possible effects of microscale curvature and roughness of real hairs on wetting, we also conduct additional experiments using biomimetic surfaces that are co-functionalised with fatty acids and sulfonate groups. In both the MD simulations and experiments, the cosine of the water contact angle increases linearly with the sulfonate group surface coverage with a similar slope. We expect that the proposed systems will be useful for future molecular dynamics simulations of the adsorption and tribological behaviour of hair, as well as other chemically heterogeneous surfaces.

Computational Indicator Approach for Assessment of Nanotoxicity of Two-Dimensional Nanomaterials

The increasing growth in the development of various novel nanomaterials and their biomedical applications has drawn increasing attention to their biological safety and potential health impact. The most commonly used methods for nanomaterial toxicity assessment are based on laboratory experiments. In recent years, with the aid of computer modeling and data science, several in silico methods for the cytotoxicity prediction of nanomaterials have been developed. An affordable, cost-effective numerical modeling approach thus can reduce the need for in vitro and in vivo testing and predict the properties of designed or developed nanomaterials. We propose here a new in silico method for rapid cytotoxicity assessment of two-dimensional nanomaterials of arbitrary chemical composition by using free energy analysis and molecular dynamics simulations, which can be expressed by a computational indicator of nanotoxicity (CIN_2D). We applied this approach to five well-known two-dimensional nanomaterials promising for biomedical applications: graphene, graphene oxide, layered double hydroxide, aloohene, and hexagonal boron nitride nanosheets. The results corroborate the available laboratory biosafety data for these nanomaterials, supporting the applicability of the developed method for predictive nanotoxicity assessment of two-dimensional nanomaterials.

High Directional Water Transport Graphene Oxide Biphilic Stack

Understanding the nature of water transport in nanoscale is of high importance. Graphene properties such as mass flow rate, stability, filtration efficiency, and selectivity have been studied in various fields. It is a widely held view that the hydrophilicity of graphene oxide enhances the water transport properties. In this study, it is shown that despite this belief, a combination of graphene and graphene oxide can yield superior transport properties including high mass flow rate and directionality. Firstly, different membrane characteristics such as the smallest pore diameter for water molecules sieving and mass flow rate have been evaluated. Furthermore, a combination of graphene and graphene oxide, a biphilic stack of hydrophobic and hydrophilic layers, are used to evaluate the mass flow rates and results are compared with that of normal graphene oxide laminates. The proposed structure acts like a water diode i.e. conduct water molecules in a desired direction and increases the mass flow rate several times. The effect of interatomic potential, oxidation level and charge, and the spacing between layers on both mass flow rate and directionality are examined. It is found that an optimized structure conducts water in a desired direction and increases the mass flow rate up to 10 times for the small interlayer distance of 7 Å compared to the normal graphene oxide laminates. The given structures can be used in a wide range of filtration applications where selective water sieving with high mass flow rate is desired.

Competitive and/or cooperative interactions of graphene-family materials and benzo[a]pyrene with pulmonary surfactant: a computational and experimental study

BACKGROUND

Airborne nanoparticles can be inhaled and deposit in human alveoli, where pulmonary surfactant (PS) molecules lining at the alveolar air-water interface act as the first barrier against inhaled nanoparticles entering the body. Although considerable efforts have been devoted to elucidate the mechanisms underlying nanoparticle-PS interactions, our understanding on this important issue is limited due to the high complexity of the atmosphere, in which nanoparticles are believed to experience transformations that remarkably change the nanoparticles' surface properties and states. By contrast with bare nanoparticles that have been extensively studied, relatively little is known about the interactions between PS and inhaled nanoparticles which already adsorb contaminants. In this combined experimental and computational effort, we investigate the joint interactions between PS and graphene-family materials (GFMs) with coexisting benzo[a]pyrene (BaP).

RESULTS

Depending on the BaP concentration, molecular agglomeration, and graphene oxidation, different nanocomposite structures are formed via BaPs adsorption on GFMs. Upon deposition of GFMs carrying BaPs at the pulmonary surfactant (PS) layer, competition and cooperation of interactions between different components determines the interfacial processes including BaP solubilization, GFM translocation and PS perturbation. Importantly, BaPs adsorbed on GFMs are solubilized to increase BaP's bioavailability. By contrast with graphene adhering on the PS layer to release part of adsorbed BaPs, more BaPs are released from graphene oxide, which induces a hydrophilic pore in the PS layer and shows adverse effect on the PS biophysical function. Translocation of graphene across the PS layer is facilitated by BaP adsorption through segregating it from contact with PS, while translocation of graphene oxide is suppressed by BaP adsorption due to the increase of surface hydrophobicity. Graphene extracts PS molecules from the layer, and the resultant PS depletion declines with graphene oxidation and BaP adsorption.

CONCLUSION

GFMs showed high adsorption capacity towards BaPs to form nanocomposites. Upon deposition of GFMs carrying BaPs at the alveolar air-water interface covered by a thin PS layer, the interactions of GFM-PS, GFM-BaP and BaP-PS determined the interfacial processes of BaP solubilization, GFM translocation and PS perturbation.

Mechanical Properties and Deformation Mechanisms of Graphene Foams with Bi-Modal Sheet Thickness by Coarse-Grained Molecular Dynamics Simulations

Graphene foams (GrFs) have been widely used as structural and/or functional materials in many practical applications. They are always assembled by thin and thick graphene sheets with multiple thicknesses; however, the effect of this basic structural feature has been poorly understood by existing theoretical models. Here, we propose a coarse-grained bi-modal GrF model composed of a mixture of 1-layer flexible and 8-layer stiff sheets to study the mechanical properties and deformation mechanisms based on the mesoscopic model of graphene sheets (Model. Simul. Mater. Sci. Eng. 2011, 19, 54003). It is found that the modulus increases almost linearly with an increased proportion of 8-layer sheets, which is well explained by the mixture rule; the strength decreases first and reaches the minimum value at a critical proportion of stiff sheets ~30%, which is well explained by the analysis of structural connectivity and deformation energy of bi-modal GrFs. Furthermore, high-stress regions are mainly dispersed in thick sheets, while large-strain areas mainly locate in thin ones. Both of them have a highly uneven distribution in GrFs due to the intrinsic heterogeneity in both structures and the mechanical properties of sheets. Moreover, the elastic recovery ability of GrFs can be enhanced by adding more thick sheets. These results should be helpful for us to understand and further guide the design of advanced GrF-based materials.

Two-Dimensional MFI Zeolite Nanosheets Exfoliated by Surfactant Assisted Solution Process

Two-dimensional (2D) zeolite nanosheets are important for the synthesis of high flux zeolite membranes due to their lateral size in a preferred orientation. A way to obtain 2D zeolite nanosheets is to exfoliate interlocked structures generated during the hydrothermal synthesis. The mechanical and polymer assisted exfoliation process leads to mechanical damage in nanosheets and short lateral size. In the present study, polyvinylpyrrolidone (PVP) was introduced as an exfoliation agent and dispersant, so that multilamellar interlocked silicalite-1 zeolite nanosheets successfully exfoliated into a large lateral size (individual nanosheets 500~1200 nm). The good exfoliation behavior was due to the strong penetration of PVP into multilamellar nanosheets. Sonication assisted by mild milling helps PVP molecules to penetrate through the lamellar structure, contributing to the expansion of the distance between adjacent layers and thus decreasing the interactions between each layer. In addition, the stability of exfoliated nanosheets was evaluated with a series of organic solvents. The exfoliated nanosheets were well dispersed in n-butanol and stable for 30 days. Therefore, the PVP-assisted solution-based exfoliation process provides high aspect ratio MFI zeolite nanosheets in organic solvents for a long period.

Antipathogenic properties and applications of low-dimensional materials

A major health concern of the 21st century is the rise of multi-drug resistant pathogenic microbial species. Recent technological advancements have led to considerable opportunities for low-dimensional materials (LDMs) as potential next-generation antimicrobials. LDMs have demonstrated antimicrobial behaviour towards a variety of pathogenic bacterial and fungal cells, due to their unique physicochemical properties. This review provides a critical assessment of current LDMs that have exhibited antimicrobial behaviour and their mechanism of action. Future design considerations and constraints in deploying LDMs for antimicrobial applications are discussed. It is envisioned that this review will guide future design parameters for LDM-based antimicrobial applications.

The Martini Model in Materials Science

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.

Hydrangea-like Superstructured Micro/Nanoreactor of Topotactically Converted Ultrathin Bismuth Nanosheets for Highly Active CO2 Electroreduction to Formate

An electrocatalytic carbon dioxide reduction reaction (CO₂RR) is an appealing route to obtain the value-added feedstocks and alleviate the energy crisis. However, how to achieve high-performance electrocatalysts for CO₂ reduction to formate is challenging owing to the poor intrinsic activity, insufficient conductivity, and low surface density of active sites. Herein, we fabricated an extremely active and selective hydrangea-like superstructured micro/nanoreactor of ultrathin bismuth nanosheets through an in situ electrochemical topotactic transformation of hierarchical bismuth oxide formate (BiOCOOH). The resulted bismuth nanosheet superstructure is in the form of three-dimensional intercrossed networks of ultrathin nanosheets, forming an ordered open porous structure through self-assembly, which can be used as a micro/nanoreactor to enable a large electrochemically active surface area as well as high atomic utilization. Such a distinctive nanostructure endows the material with high electrocatalytic performances for CO₂ reduction to formate with near-unity Faradaic selectivity (>95%) in a wide potential window from -0.78 to -1.18 V. Furthermore, this micro/nanoreactor can give the high current densities over 300 mA cm^-2 at low applied potentials without compromising selectivity in a flow cell reactor. Density functional theory (DFT) and in situ attenuated total reflection-infrared spectroscopy (in situ ATR-IR) were further conducted to interpret the CO₂RR mechanisms.

Environmental risk of nanomaterials and nanoparticles and EPR technique as an effective tool to study them-a review

Nanotechnologies and different types of nanomaterials belong in present day to intensively studied materials due to their unique properties and diverse potential applications in, e.g., electronics, medicine, or display technologies. Together with the investigation of their desired beneficial properties, a need to investigate and evaluate their influence on the environment and possible harmful effects towards living organisms is growing. This review summarizes possible toxic effects of nanomaterials on environment and living organisms, focusing on the possible bioaccumulation in organisms, toxicity, and its mechanisms. The main goal of this review is to refer to potential environmental risks rising from the use of nanomaterials and the necessity to deal with the possible toxic effects considering the growing interest in the wide-scale utilization of these materials. Electron paramagnetic resonance spectroscopy as the only analytical technique capable of detecting radical species enables detection, quantification, and monitoring of the generation of short-lived radicals often coupled with toxic effects of nanomaterials, which makes it an important method in the process of nanotoxicity mechanism determination.

Effect of Shape on the Entering of Graphene Quantum Dots into a Membrane: A Molecular Dynamics Simulation

Graphene quantum dots (GQDs), a new quasi-zero-dimensional nanomaterial, have the advantages of a smaller transverse size, better biocompatibility, and lower toxicity. They have potential applications in biosensors, drug delivery, and biological imaging. Therefore, it is particularly important to understand the transport mechanism of the GQDs on the cell membrane. In particular, the effect of the GQD shapes on the translocation mechanism should be well understood. In this study, the permeation process of the GQDs with different shapes through a 1-palmitoyl-2-oleoylphosphatidylcholine membrane was studied using molecular dynamics. The results show that all small-sized GQDs with different shapes translocated through the lipid membrane at a nanosecond timescale. The GQDs tend to remain on the surface of the cell membrane; then, the corners of the GQDs spontaneously enter the cell membrane; and, finally, the entire GQDs enter the cell membrane and tend to stabilize in the middle of the cell membrane. Moreover, the GQDs do not induce notable damage to the cell membrane, indicating that they are less toxic to cells and can be used as a potential biomedical material.

Hybridization of Biomolecular Crystals and Low-Dimensional Materials

In cellular environments, metabolites, peptides, proteins, and other biomolecules can self-assemble into planar and fibrilar molecular crystals. We use atomistic molecular dynamics simulations to show that such biomolecular crystals coupled with low-dimensional materials can form stable hybrid superstructures. We discuss enantiopure and racemic TRP and PHE amino acid crystals adsorbed on or intercalated between graphene, phosphorene, and carbon nanotubes. While racemic biomolecular crystals tend to stay straight in solutions and when adsorbed on flat and cylindrical nanosurfaces, enantiopure crystals undergo twisting. Mixed material properties of these hybrid superstructures can be attractive in many applications.

Graphene Sheets with Defined Dual Functionalities for the Strong SARS-CoV-2 Interactions

Search of new strategies for the inhibition of respiratory viruses is one of the urgent health challenges worldwide, as most of the current therapeutic agents and treatments are inefficient. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic and has taken lives of approximately two million people to date. Even though various vaccines are currently under development, virus, and especially its spike glycoprotein can mutate, which highlights a need for a broad-spectrum inhibitor. In this work, inhibition of SARS-CoV-2 by graphene platforms with precise dual sulfate/alkyl functionalities is investigated. A series of graphene derivatives with different lengths of aliphatic chains is synthesized and is investigated for their ability to inhibit SARS-CoV-2 and feline coronavirus. Graphene derivatives with long alkyl chains (>C9) inhibit coronavirus replication by virtue of disrupting viral envelope. The ability of these graphene platforms to rupture viruses is visualized by atomic force microscopy and cryogenic electron microscopy. A large concentration window (10 to 100-fold) where graphene platforms display strongly antiviral activity against native SARS-CoV-2 without significant toxicity against human cells is found. In this concentration range, the synthesized graphene platforms inhibit the infection of enveloped viruses efficiently, opening new therapeutic and metaphylactic avenues against SARS-CoV-2.

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.

Molecular mechanisms underlying the role of the puckered surface in the biocompatibility of black phosphorus

As a newly emerging two-dimensional material, black phosphorus (BP) has received broad attention in the field of biomedical applications. Prior to its clinical application, its cytotoxicity to cells should be carefully evaluated; however, this field is still in its infancy. Motivated by this, we performed molecular dynamics (MD) simulations to systematically investigate the potential mechanisms of the cytotoxicity of BP to the lipid membrane, including lipid extraction, penetration into the membrane, and the impacts of BP on the physical properties of the membrane. Surprisingly, we observed that BP could not extract lipid molecules from the membrane. The thermodynamic analyses suggested that the puckered surface structure could weaken the interactions between BP and lipid molecules, thus inhibiting the lipid extraction. Additionally, through simulating the spontaneous interaction modes between BP and the lipid membrane, we found that the "passivated" edges of BP prohibited it from penetrating into the membrane. As a result, BP could only spontaneously lie parallel on the surface of the membrane, in which manner BP exerted little influence on the properties of the lipid membrane. To comprehensively appraise the cytotoxicity, we even artificially inserted BP into the membrane and compared the effects of BP and graphene on the properties of the membrane. Simulation results showed that the influences of the inserted BP on the lipid properties were much milder than those of graphene. Overall, the present work suggests that BP possesses distinctive biocompatibility benefiting from its puckered surface structure. This work provides a better understanding of the interactions between BP and the membrane, which may offer some useful suggestions for exploring strategies to improve the biocompatibility of nanomaterials.

Encapsulation of Graphene in the Hydrophobic Core of a Lipid Bilayer

Theoretical simulations have predicted that a lipid bilayer forms a stable superstructure when a sheet of graphene is inserted in its hydrophobic core. We experimentally produced for the first time a lipid-graphene-lipid assembly by combining the Langmuir-Blodgett and the Langmuir-Schaefer methods. Graphene is sandwiched and remains flat within the hydrophobic core of the lipid bilayer. Using infrared spectroscopy, ellipsometry, and neutron reflectometry, we characterized the superstructure at every fabrication step. The hybrid superstructure is mechanically stable and graphene does not disturb the natural lipid bilayer structure.

Enhanced Chemotherapy for Glioblastoma Multiforme Mediated by Functionalized Graphene Quantum Dots

Glioblastoma is the most aggressive and lethal brain cancer. Current treatments involve surgical resection, radiotherapy and chemotherapy. However, the life expectancy of patients with this disease remains short and chemotherapy leads to severe adverse effects. Furthermore, the presence of the blood–brain barrier (BBB) makes it difficult for drugs to effectively reach the brain. A promising strategy lies in the use of graphene quantum dots (GQDs), which are light-responsive graphene nanoparticles that have shown the capability of crossing the BBB. Here we investigate the effect of GQDs on U87 human glioblastoma cells and primary cortical neurons. Non-functionalized GQDs (NF-GQDs) demonstrated high biocompatibility, while dimethylformamide-functionalized GQDs (DMF-GQDs) showed a toxic effect on both cell lines. The combination of GQDs and the chemotherapeutic agent doxorubicin (Dox) was tested. GQDs exerted a synergistic increase in the efficacy of chemotherapy treatment, specifically on U87 cells. The mechanism underlying this synergy was investigated, and it was found that GQDs can alter membrane permeability in a manner dependent on the surface chemistry, facilitating the uptake of Dox inside U87 cells, but not on cortical neurons. Therefore, experimental evidence indicates that GQDs could be used in a combined therapy against brain cancer, strongly increasing the efficacy of chemotherapy and, at the same time, reducing its dose requirement along with its side effects, thereby improving the life quality of patients.

Graphene Quantum Dots' Surface Chemistry Modulates the Sensitivity of Glioblastoma Cells to Chemotherapeutics

Recent evidence has shown that graphene quantum dots (GQDs) are capable of crossing the blood-brain barrier, the barrier that reduces cancer therapy efficacy. Here, we tested three alternative GQDs' surface chemistries on two neural lineages (glioblastoma cells and mouse cortical neurons). We showed that surface chemistry modulates GQDs' biocompatibility. When used in combination with the chemotherapeutic drug doxorubicin, GDQs exerted a synergistic effect on tumor cells, but not on neurons. This appears to be mediated by the modification of membrane permeability induced by the surface of GQDs. Our findings highlight that GQDs can be adopted as a suitable delivery and therapeutic strategy for the treatment of glioblastoma, by both directly destabilizing the cell membrane and indirectly increasing the efficacy of chemotherapeutic drugs.

Engineering of 2D Ti3C2 MXene Surface Charge and Its Influence on Biological Properties

Current trends in the field of MXenes emphasize the importance of controlling their surface features for successful application in biotechnological areas. The ability to stabilize the surface properties of MXenes has been demonstrated here through surface charge engineering. It was thus determined how changing the surface charges of two-dimensional (2D) Ti₃C₂ MXene phase flakes using cationic polymeric poly-L-lysine (PLL) molecules affects the colloidal and biological properties of the resulting hybrid 2D nanomaterial. Electrostatic adsorption of PLL on the surface of delaminated 2D Ti₃C₂ flakes occurs efficiently, leads to changing an MXene's negative surface charge toward a positive value, which can also be effectively managed through pH changes. Analysis of bioactive properties revealed additional antibacterial functionality of the developed 2D Ti₃C₂/PLL MXene flakes concerning Escherichia. coli Gram-negative bacteria cells. A reduction of two orders of magnitude of viable cells was achieved at a concentration of 200 mg L^-1. The in vitro analysis also showed lowered toxicity in the concentration range up to 375 mg L^-1. The presented study demonstrates a feasible approach to control surface properties of 2D Ti₃C₂ MXene flakes through surface charge engineering which was also verified in vitro for usage in biotechnology or nanomedicine applications.

Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide

The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A₁₂, C₁₂, G₁₂, and T₁₂) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide-GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T₁₂) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T₁₂ was more likely to form a quasi-parallel structure with GO compared to A₁₂, C₁₂, or G₁₂. This was attributed to the weakest π-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T₁₂ and the GO surface enabled T₁₂ to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.

Diffusive transport of nanoscale objects through cell membranes: a computational perspective

Diffusion is an essential and fundamental means of transport of substances on cell membranes, and the dynamics of biomembranes plays a crucial role in the regulation of numerous cellular processes. The understanding of the complex mechanisms and the nature of particle diffusion have a bearing on establishing guidelines for the design of efficient transport materials and unique therapeutic approaches. Herein, this review article highlights the most recent advances in investigating diffusion dynamics of nanoscale objects on biological membranes, focusing on the approaches of tailored computer simulations and theoretical analysis. Due to the presence of the complicated and heterogeneous environment on native cell membranes, the diffusive transport behaviors of nanoparticles exhibit unique and variable characteristics. The general aspects and basic theories of normal diffusion and anomalous diffusion have been introduced. In addition, the influence of a series of external and internal factors on the diffusion behaviors is discussed, including particle size, membrane curvature, particle-membrane interactions or particle-inclusion, and the crowding degree of membranes. Finally, we seek to identify open problems in the existing experimental, simulation, and theoretical research studies, and to propose challenges for future development.

Length feature of ssDNA adsorption onto graphene oxide with both large unoxidized and oxidized regions

DNA/GO functional structures have been widely used in biosensors, biomedicine and materials science. However, most studies about DNA/GO functional structures do not take into account the coexistence of both large unoxidized and oxidized regions on GO sheets. This special local structure provides the boundary region, which is the junction area between unoxidized and oxidized regions, and exhibits a special amphiphilic property of the GO sheets. Here based on molecular dynamics simulations, our results predict that the adsorption efficiency of long strand ssDNA molecules adsorbed on GO is 43%. Further analysis has shown that the ssDNA adsorption behaviors on the GO surface are more likely to start in the boundary region, even for 20 mer ssDNA molecules. Looking into the adsorption dynamic process we can see that the hydrogen bonds between ssDNA and GO are very active and easily broken and formed, especially for the boundary region of the GO surface, resulting in easy capture and adsorption of the ssDNA molecules on this region. The result provides insightful understanding of the adsorption behavior of ssDNA molecules on this amphiphilic GO surface and is helpful in the design of DNA/GO functional structure-based biosensors.

Atomistic and coarse-grained simulations of membrane proteins: A practical guide

Membrane proteins are amphipathic macromolecules whose exposed hydrophobic surfaces promote interactions with lipid membranes. Membrane proteins are remarkably diverse in terms of chemical composition and correspondingly, their biological functions and general biophysical behavior. Conventional experimental techniques provide an approach to study specific properties of membrane proteins e.g. their surface features, the nature and abundance of stabilizing intramolecular forces, preferred bilayer orientation, and the characteristics of their annular lipid shells. Molecular modeling software-and in particular, the suite of molecular dynamics algorithms-enables a more comprehensive exploration of dynamic membrane protein behavior. Molecular dynamics methods enable users to produce stepwise trajectories of proteins on arbitrary spatiotemporal scales that enable the easy identification of dynamic interactions that are beyond the scope of conventional analytical techniques. This article explains the molecular dynamics theoretical framework and popular step-by-step approaches for simulating membrane proteins in planar, and to a lesser extent, nonplanar lipid geometries. We detail popular procedures and computational tools that produce well-packed configurations of lipids and proteins and additionally, the efficient molecular dynamics simulation algorithms that reproduce their dynamic interactions.

Pushing Rubbery Polymer Membranes To Be Economic for CO2 Separation: Embedment with Ti3C2Tx MXene Nanosheets

Sustainable and energy-efficient molecular separation requires membranes with high gas permeability and selectivity. This work reports excellent CO₂ separation performance of self-standing and thin-film mixed matrix membranes (MMMs) fabricated by embedding 2D Ti₃C₂T_x MXene nanosheets in Pebax-1657. The CO₂/N₂ and CO₂/H₂ separation performances of the free-standing membranes are above Robeson's upper bounds, and the performances of the thin-film composite (TFC) membranes are in the target area for cost-efficient CO₂ capture. Characterization and molecular dynamics simulation results suggest that the superior performances of the Pebax-Ti₃C₂T_x membranes are due to the formation of hydrogen bonds between Ti₃C₂T_x and Pebax chains, leading to the creation of the well-formed galleries of Ti₃C₂T_x nanosheets in the hard segments of the Pebax. The interfacial interactions and selective Ti₃C₂T_x nanochannels enable fast and selective CO₂ transport. Enhancement of the transport properties of Pebax-2533 and polyurethane when embedded with Ti₃C₂T_x further supports these findings. The ease of fabrication and high separation performance of the new TFC membranes point to their great potential for energy-efficient CO₂ separation with the low cost of $29/ton separated CO₂.

Interaction of Graphene Nanoparticles and Lipid Membranes Displaying Different Liquid Orderings: A Molecular Dynamics Study

Understanding the effects of graphene-based nanomaterials on lipid membranes is fundamental to determine their environmental impact and the efficiency of their biomedical use. By means of molecular dynamics simulations of simple model lipid bilayers, we analyze in detail the different interaction modes. We have studied bilayers consisting of lipid species (including cholesterol) which display different internal liquid orderings. Nanometric graphene layers can be transiently adsorbed onto the lipid membrane and/or inserted in its hydrophobic region. Once inserted, graphene nanometric flakes display a diffusive dynamics in the membrane plane, they adopt diverse orientations depending on their size and oxidation degree, and they show a particular aversion to be placed close to cholesterol molecules in the membrane. Addition of graphene to phase-segregated ternary membranes is also investigated in the context of the lipid raft model for the lipid organization of biological membranes. Our simulation results show that graphene layers can be inserted indistinctly in the ordered and disordered regions. Once inserted, nanometric flakes migrate to disordered and cholesterol-poor lipid phases.

Understanding the Synergic Mechanism of Weak Interactions between Graphene Oxide and Lipid Membrane Leading to the Extraction of Lipids

Revealing how weak forces interact synergistically to induce differences in nanobio effects is critical to understanding the nature of the nanobio interface. Herein, graphene oxide (GO) and a lipid membrane are selected as a nanobio model, and interaction forces at the GO-biomembrane interface are modulated by varying the amounts and species of oxygenated functional groups on the surface of GO. A synergic mechanism of interfacial interaction forces is investigated by a combination of surface-enhanced infrared absorption (SEIRA) spectroscopy, confocal laser scanning microscopy (CLSM), and electrochemical impedance spectroscopy (EIS). The results reveal that after balancing with electrostatic repulsion, the moderate attraction between GO and lipid headgroups (such as electrostatic and/or hydrophobic interactions) is most favorable for lipid extraction, whereas lipid extraction is inhibited under an attraction that is too strong or too weak. Under moderate attraction between GO and the headgroups of lipids, the appropriate degree of rotation freedom is maintained for GO, which is beneficial to the hydrogen-bonding interaction between the C═O group in the phosphatide hydrophobic region and GO, thus triggering the insertion of GO into the lipid alkyl chain region, resulting in the rapid and significant extraction of lipids. Our results have important guiding significance for how to reveal the synergistic mechanism of weak interactions at the nanobio interface.

Functionalized nanographene sheets with high antiviral activity through synergistic electrostatic and hydrophobic interactions

As resistance to traditional drugs emerges for treatment of virus infections, the need for new methods for virus inhibition increases. Graphene derivatives with large surface areas have shown strong activity against different viruses. However, the inability of current synthetic protocols to accurately manipulate the structure of graphene sheets in order to control their antiviral activity remains a major challenge. In this work, a series of graphene derivatives with defined polyglycerol sulfate and fatty amine functionalities have been synthesized and their interactions with herpes simplex virus type 1 (HSV-1) are investigated. While electrostatic interactions between polyglycerol sulfate and virus particles trigger the binding of graphene to virus, alkyl chains induce a high antiviral activity by secondary hydrophobic interactions. Among graphene sheets with a broad range of alkyl chains, (C3-C18), the C12-functionalized sheets showed the highest antiviral activity, indicating the optimum synergistic effect between electrostatic and hydrophobic interactions, but this derivative was toxic against the Vero cell line. In contrast, sheets functionalized with C6- and C9-alkyl chains showed low toxicity against Vero cells and a synergistic inhibition of HSV-1. This study shows that antiviral agents against HSV-1 can be obtained by controlled and stepwise functionalization of graphene sheets and may be developed into antiviral agents for future biomedical applications.

Graphene-Based Nanomaterials: From Production to Integration With Modern Tools in Neuroscience

Graphene, a two-dimensional carbon crystal, has emerged as a promising material for sensing and modulating neuronal activity in vitro and in vivo. In this review, we provide a primer for how manufacturing processes to produce graphene and graphene oxide result in materials properties that may be tailored for a variety of applications. We further discuss how graphene may be composited with other bio-compatible materials of interest to make novel hybrid complexes with desired characteristics for bio-interfacing. We then highlight graphene's ever-widen utility and unique properties that may in the future be multiplexed for cross-modal modulation or interrogation of neuronal network. As the biological effects of graphene are still an area of active investigation, we discuss recent development, with special focus on how surface coatings and surface properties of graphene are relevant to its biological effects. We discuss studies conducted in both non-murine and murine systems, and emphasize the preclinical aspect of graphene's potential without undermining its tangible clinical implementation.

Transport of a graphene nanosheet sandwiched inside cell membranes

The transport of nanoparticles at bio-nano interfaces is essential for many cellular responses and biomedical applications. How two-dimensional nanomaterials, such as graphene and transition-metal dichalcogenides, diffuse along the cell membrane is, however, unknown, posing an urgent and important issue to promote their applications in the biomedical area. Here, we show that the transport of graphene oxides (GOs) sandwiched inside cell membranes varies from Brownian to Lévy and even directional dynamics. Specifically, experiments evidence sandwiched graphene-cell membrane superstructures in different cells. Combined simulations and analysis identify a sandwiched GO-induced pore in cell membrane leaflets, spanning unstable, metastable, and stable states. An analytical model that rationalizes the regimes of these membrane-pore states fits simulations quantitatively, resulting in a mechanistic interpretation of the emergence of Lévy and directional dynamics. We finally demonstrate the applicability of sandwiched GOs in enhanced efficiency of membrane-specific drug delivery. Our findings inform approaches to programming intramembrane transport of two-dimensional nanomaterials toward advantageous biomedical applications.