Orientational Binding of DNA Guided by the C2N Template

Patterned graphene: An effective platform for adsorption, immobilization, and destruction of SARS-CoV-2 Mpro

To address the ongoing challenges posed by the SARS-CoV-2 and potentially stronger viruses in the future, the development of effective methods to fabricate patterned graphene (PG) and other precisely functional products has become a new research frontier. Herein, we modeled the "checkerboard" graphene (CG) and stripped graphene (SG) as representatives of PG, and studied their interaction mechanism with the target protein (Mpro) by molecular dynamics simulation. The calculation results on the binding strength and the root mean square deviation values of the active pocket revealed that PG is an effective platform for adsorption, immobilization, and destruction of Mpro. Specifically, CG is found to promote disruption of the active pocket for Mpro, but the presence of "checkerboard" oxidized regions inhibits the adsorption of Mpro. Meanwhile, the SG can effectively confine Mpro within the non-oxidized strips and enhances their binding strength, but doesn't play well on disrupting the active pocket. Our work not only elucidates the biological effects of PGs, but also provides guidance for their targeted and precise utilization in combating the SARS-CoV-2.

Directional Pumpless Transport of Biomolecules through Self-Propelled Nanodroplets on Patterned Heterostructures

The surface patterning in natural systems has exhibited appreciable functional advantages for life activities, which serve as inspiration for the design of artificial counterparts to achieve functions such as directional liquid transport at the nanoscale. Here, we propose a patterned two-dimensional (2D) in-plane heterostructure with a triangle-shaped hexagonal boron nitride (hBN) track embedded in graphene nanosheets, which can achieve unidirectional and self-propelled transport of nanodroplets carrying various biomolecules such as DNA, RNA, and peptides. Our extensive MD simulations show that the wettability gradient on the patterned heterostructure can drive the motion of nanodroplet with an instantaneous acceleration, which also permits long-distance transport (>100 nm) at the microsecond time scale. The different behaviors of various types of biomolecules have been further studied systematically within the transporting nanodroplets. These findings suggest that these specially designed, patterned heterostructures have the potential for spontaneous, directional transport of important biomolecules, which might be useful in biosensing, drug delivery, and biomedical nanodevices.

Detecting Hachimoji DNA: An Eight-Building-Block Genetic System with MoS2 and Janus MoSSe Monolayers

In the pursuit of personalized medicine, the development of efficient, cost-effective, and reliable DNA sequencing technology is crucial. Nanotechnology, particularly the exploration of two-dimensional materials, has opened different avenues for DNA nucleobase detection, owing to their impressive surface-to-volume ratio. This study employs density functional theory with van der Waals corrections to methodically scrutinize the adsorption behavior and electronic band structure properties of a DNA system composed of eight hachimoji nucleotide letters adsorbed on both MoS2 and MoSSe monolayers. Through a comprehensive conformational search, we pinpoint the most favorable adsorption sites, quantifying their adsorption energies and charge transfer properties. The analysis of electronic band structure unveils the emergence of flat bands in close proximity to the Fermi level post-adsorption, a departure from the pristine MoS2 and MoSSe monolayers. Furthermore, leveraging the nonequilibrium Green's function approach, we compute the current-voltage characteristics, providing valuable insights into the electronic transport properties of the system. All hachimoji bases exhibit physisorption with a horizontal orientation on both monolayers. Notably, base G demonstrates high sensitivity on both substrates. The obtained current-voltage (I-V) characteristics, both without and with base adsorption on MoS2 and the Se side of MoSSe, affirm excellent sensing performance. This research significantly advances our understanding of potential DNA sensing platforms and their electronic characteristics, thereby propelling the endeavor for personalized medicine through enhanced DNA sequencing technologies.

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

Since the discovery of graphene, two-dimensional (2D) materials have been anticipated to demonstrate enormous potential in bionanomedicine. Unfortunately, the majority of 2D materials induce nanotoxicity via disruption of the structure of biomolecules. Consequently, there has been an urge to synthesize and identify biocompatible 2D materials. Before the cytotoxicity of 2D nanomaterials is experimentally tested, computational studies can rapidly screen them. Additionally, computational analyses can provide invaluable insights into molecular-level interactions. Recently, various "in silico" techniques have identified these interactions and helped to develop a comprehensive understanding of nanotoxicity of 2D materials. In this article, we discuss the key recent advances in the application of computational methods for the screening of 2D materials for their nanotoxicity toward two important categories of abundant biomolecules, namely, nucleic acids and proteins. We believe the present article would help to develop newer computational protocols for the identification of novel biocompatible materials, thereby paving the way for next-generation biomedical and therapeutic applications based on 2D materials.

Computational Assessment of the Biocompatibility of Two-Dimensional g-C3N3 Toward Lipid Membranes

One of the most recent additions to the family of two-dimensional (2D) materials, graphitic C3N3 (g-C3N3), has been considered a viable contender for biomedical applications, although its potential toxicity remains elusive. We perform all-atom molecular dynamics simulations to decipher the interactions between model lipid membranes and g-C3N3 as a first step toward exploring the cytotoxicity induced at the nanoscale. We show that g-C3N3 can easily insert into the cellular membranes following a multistage mechanism consisting of simultaneous desolvation of the 2D material along with enrichment of nanomaterial-lipid interactions. Free energy calculations indicate that g-C3N3 is more stable in a membrane-bound state compared to an aqueous solution; however, the insertion of the material does not disturb the structural integrity of lipid membranes. After being inserted into a membrane, g-C3N3 is unlikely to be released into the cellular environment and is incapable of extracting lipid molecules from the membrane. The nature of interaction between the 2D material and membranes is found to be independent of the nanomaterial size. Also, the performance of g-C3N3 toward biomolecular delivery is shown to be significantly improved compared to the state-of-the-art 2D materials graphene and hexagonal boron nitride (h-BN). It is revealed that, the affinity of g-C3N3 toward lipid membranes is weaker compared to the nanotoxic graphene and h-BN, while being marginally higher than h2D-C2N, which in turn, increases the biocompatibility of the material, thereby brightening its future as a noncytotoxic material for forthcoming biomedical applications.

Better biocompatibility of nitrogen-doped graphene compared with graphene oxide by reducing cell autophagic flux blockage and cell apoptosis

Nitrogen-doped graphene (C2 N), a novel graphene-based materials, has been proposed as a potential alternative to graphene oxide (GO) in biomedical applications. However, due to the challenges in synthesizing C2 N, reports in the biomedical field are currently rare. Here, we have modified the reported procedure and successfully synthesized C2 N nanoparticles at 120°C, which we refer to as C2 N-120. The toxicity and biocompatibility of GO and C2 N-120 were evaluated using a mouse model injected with GO/C2 N-120 via the tail vein, as well as cell models treated with GO/C2 N-120. In vivo studies revealed that GO/C2 N-120 showed similar distribution patterns after tail vein injection. The liver, spleen, and lung are the major nanoparticle uptake organs of GO and C2 N-120. However, GO deposition in the major nanoparticle uptake organs was more significant than that of C2 N-120. In addition, GO deposition caused structural abnormalities, increased apoptotic cells, and enhanced macrophage infiltration whereas C2 N-120 exhibited fewer adverse effects. In vitro experiments were conducted using different cell lines treated with GO/C2 N-120. Unlike GO which induced mitochondrial damage, oxidative stress, inflammatory response, autophagic flux blockage and cell apoptosis, C2 N-120 showed lower cytotoxicity in cell models. Our data demonstrated that C2 N-120 exhibits higher biocompatibility than GO, both in vivo and in vitro, suggesting its potential for biomedical application in the future.

Size- and Voltage-Dependent Electron Transport of C2N-Rings-Based Molecular Chains

C2N-ring-based molecular chains were designed at the molecular level and theoretically demonstrated to show distinctive and valuable electron transport properties that were superior to the parent carbonaceous system and other similar nanoribbon-based molecular chains. This new -type molecular chain presented an exponential attenuation of the conductance and electron transmission with the length. Essentially, the molecular chain retained the electron-resonant tunneling within 7 nm and the dominant transport orbital was the LUMO. Shorter molecular chains with stronger conductance anomalously possessed a larger tunnel barrier energy, attributing to the compensation of a much smaller HOMO-LUMO gap, and these two internal factors codetermined the transport capacity. Some influencing factors were also studied. In contrast to the common O impurity with a tiny effect on electron transmission of the C2N rings chain, the common H impurity clearly improved it. When the temperature was less than 400 K, the electron transmission varied with temperature within a narrow range, and the structural disorder deriving from proper heating did not greatly modify the transmission possibility and the exponentially decreasing tendency with the length. In a non-equilibrium condition, the current increased overall with the bias but the growth rate varied with size. A valuable negative differential resistance (NDR) effect appeared in longer molecular chains with an even number of big carbon-nitrogen rings and strengthened with size. The emergence of such an effect originated from the reduction in transmission peaks. The conductance of longer molecular chains was enhanced with the voltage but the two shortest ones presented completely different trends. Applying the bias was demonstrated to be an effective way for C2N-ring-based molecular chains to slow down the conductance decay constant and affect the transport regime. C2N-ring-based molecular chains show a perfect application in tunneling diodes and controllable molecular devices.

Curvature induced structural changes of the chicken villin headpiece subdomain by single walled carbon nanotubes

Carbon nanotubes (CNTs) are identified as potential candidates for drug and biomolecular loading and delivery. CNTs of different chiralities have different diameters, which may significantly affect their abilities to interact with different types of biomolecules. Herein, we employ classical molecular dynamics simulation to provide insight into the curvature-dependent interactions between a model protein, chicken villin headpiece subdomain (HP36), with CNTs having chiralities (8,8), (12,12), and (20,20). It is revealed that, with increasing radii, the protein encounters more aromatic carbon atoms on the surface of the CNT, leading to its increasing strength of adsorption. However, the extent of adsorption has a limiting magnitude, after which an increase in the radius of the nanotube has practically no effect on the extent of adsorption. Spontaneous encapsulation of the protein was demonstrated using a (28,28) CNT, where the protein is found to undergo insignificant structural perturbation. Finally, steered molecular dynamics simulations have been performed to mimic the force-induced release of the protein from within the nanotube cavity. It has been identified that a minimum force of ∼300 pN and a minimum velocity of 4 Å ns-1 are required to release the protein from the CNT at 300 K. Any external force below the critical magnitude and inducing velocity less than 4 Å ns-1 allows the translocation of the protein through the inner surface of the CNT; however, before being released, the protein undergoes unfolding, thereby losing the secondary structure and biological activity.

Moderate binding of villin headpiece protein to C3N3 nanosheet reveals the suitable biocompatibility of this nanomaterial

Since its recent successful synthesis and due to its promising physical and chemical properties, the carbon nitrite nanomaterial, C3N3, has attracted considerable attention in various scientific areas. However, thus far, little effort has been devoted to investigating the structural influence of the direct interaction of this 2D nanomaterial and biomolecules, including proteins and biomembranes so as to understand the physical origin of its bio-effect, particularly from the molecular landscape. Such information is fundamental to correlate to the potential nanotoxicology of the C3N3 nanomaterial. In this work, we explored the potential structural influence of a C3N3 nanosheet on the prototypical globular protein, villin headpiece (HP35) using all-atom molecular dynamics (MD) simulations. We found that HP35 could maintain its native conformations upon adsorption onto the C3N3 nanosheet regardless of the diversity in the binding sites, implying the potential advantage of C3N3 in protecting the biomolecular structure. The adsorption was mediated primarily by vdW interactions. Moreover, once adsorbed on the C3N3 surface, HP35 remains relatively fixed on the nanostructure without a distinct lateral translation, which may aid in keeping the structural integrity of the protein. In addition, the porous topological structure of C3N3 and the special water layer present on the C3N3 holes conjointly contributed to the restricted motion of HP35 via the formation of a high free energy barrier and a steric hindrance to prevent the surface displacement. This work revealed for the first time the potential influence of the 2D C3N3 nanomaterial in the protein structure and provided the corresponding in-depth molecular-level mechanism, which is valuable for future applications of C3N3 in bionanomedicine.

A numerical model for water hydration on nanosurfaces: from friction to hydrophilicity and hydrophobicity

Fluidic transport down to the nanometer scale is of great importance for a wide range of applications such as energy harvesting, seawater desalination, and water treatment and may help to understand many biological processes. In this work, we studied the interfacial friction of liquid water on a series of nanostructures through molecular dynamics (MD) simulations. Our results reveal that the friction coefficient of the water-solid interface cannot be described using a previously reported simple function of the free energy corrugation. Considering that the water-solid friction is firmly correlated with the microscopic water motion, we proposed a probability parameter P(d, t) to classify water motion modes on a surface. We demonstrate that this parameter can be used to accurately predict the water-solid friction by simply monitoring the water binding time on a nanosurface. More importantly, according to the relationship between P(d, t) and friction, we found that the friction coefficient can be used as an indicative criterion for quantitatively assessing hydrophobic or hydrophilic materials, where the borderline is roughly 2 × 10⁵ N s m^-3. That is if the water-solid friction is less than 2 × 10⁵ N s m^-3, the surface is considered hydrophobic. But if the friction is larger than this value, the surface is hydrophilic. The present findings could help to better understand fluidic transport at the nanoscale and guide the future design of functional materials, such as super-hydrophobic and super-hydrophilic surfaces by structure engineering.

Remarkable Single Atom Catalyst of Transition Metal (Fe, Co & Ni) Doped on C2N Surface for Hydrogen Dissociation Reaction

Currently, hydrogen is recognized as the best alternative for fossil fuels because of its sustainable nature and environmentally friendly processing. In this study, hydrogen dissociation reaction is studied theoretically on the transition metal doped carbon nitride (C₂N) surface through single atom catalysis. Each TMs@C₂N complex is evaluated to obtain the most stable spin state for catalytic reaction. In addition, electronic properties (natural bond orbital NBO & frontier molecular orbital FMO) of the most stable spin state complex are further explored. During dissociation, hydrogen is primarily adsorbed on metal doped C₂N surface and then dissociated heterolytically between metal and nitrogen atom of C₂N surface. Results revealed that theFe@C₂N surface is the most suitable catalyst for H₂ dissociation reaction with activation barrier of 0.36 eV compared with Ni@C₂N (0.40 eV) and Co@C₂N (0.45 eV) complexes. The activation barrier for H₂ dissociation reaction is quite low in case of Fe@C₂N surface, which is comparatively better than already reported noble metal catalysts.

Dicarbon nitride and Janus transition metal chalcogenides van der Waals heterojunctions for photocatalytic water splitting

Two-dimensional graphene-like dicarbon nitride (C₂N) is a newly synthesized metal-free material, which has attracted significant research interest owing to the direct band gap, high carrier mobility, thermal stability, and great tunable properties. However, their application in photocatalytic water splitting has not been well explored. In this work, the properties of photocatalytic water decomposition in heterojunctions composed of C₂N and transition metal dichalcogenides (TMDs) with Janus structure MoXY (X, Y = S, Se, Te) are systematically studied by the first-principles calculations based on density functional theory. The results show that except for MoTeS/C₂N, the other five heterojunctions have type-Ⅱ band alignment, which causes electrons and holes to gather in the C₂N and MoXY layer separately. Because the coupled built-in electric field at the intra-layer and inter-layer of asymmetric TMDs with Janus structure forms van der Waals heterojunction, the external electric field is an effective means of modulating the electronic properties of the heterojunction. Under the imposition of an external electric field, the MoSeS/C₂N, MoTeSe/C₂N, and MoTeS/C₂N heterojunctions meet the band edge requirements for the photocatalytic decomposition of water. Detailed analysis demonstrates that the MoSeS/C₂N heterojunction could effectively improve the optical absorption properties of monolayer C₂N, making it a potential photocatalytic water decomposition material.

Theoretical Evaluation of Potential Cytotoxicity of Graphene Quantum Dot to Adsorbed DNA

As a zero-dimensional (0D) nanomaterial, graphene quantum dot (GQD) has a unique physical structure and electrochemical properties, which has been widely used in biomedical fields, such as bioimaging, biosensor, drug delivery, etc. Its biological safety and potential cytotoxicity to human and animal cells have become a growing concern in recent years. In particular, the potential DNA structure damage caused by GQD is of great importance but still obscure. In this study, molecular dynamics (MD) simulation was used to investigate the adsorption behavior and the structural changes of single-stranded (ssDNA) and double-stranded DNA (dsDNA) on the surfaces of GQDs with different sizes and oxidation. Our results showed that ssDNA can strongly adsorb and lay flat on the surface of GQDs and graphene oxide quantum dots (GOQDs), whereas dsDNA was preferentially oriented vertically on both surfaces. With the increase of GQDs size, more structural change of adsorbed ssDNA and dsDNA could be found, while the size effect of GOQD on the structure of ssDNA and dsDNA is not significant. These findings may help to improve the understanding of GQD biocompatibility and potential applications of GQD in the biomedical field.

On the interface between biomaterials and two-dimensional materials for biomedical applications

Two-dimensional (2D) materials have garnered significant attention due to their ultrathin 2D structures with a high degree of anisotropy and functionality. Reliable manipulation of interfaces between 2D materials and biomaterials is a new frontier for biomedical nanoscience and combining biomaterials with 2D materials offers a promising way to fabricate innovative 2D biomaterials composites with distinct functionality for biomedical applications. Here, we focus exclusively on a summary of the current work in the interface investigation of 2D biomaterials. Specifically, we highlight extraordinary features that make 2D materials so desirable, as well as the molecular level interactions between 2D materials and biomaterials that have been studied thus far. Furthermore, the approaches for investigating the interface characteristics of 2D biomaterials are presented and described in depth. To capture the emerging trend in mass manufacturing of 2D materials, we review the research progress on biomaterial-assisted exfoliation. Finally, we present a critical assessment of newly developed 2D biomaterials in biomedical applications.

Understanding the anchoring interaction of coagulation factor Va light chain on zeolites: A molecular dynamics study

HYPOTHESIS

Factor Va (FXa) and Xa (FVa) can assemble on the phosphatidylserine (PS) membrane (of platelet) to form prothrombinase complex and contribute to blood clotting. Very recently, we discovered that Ca-zeoliteacts as a type of reinforced activated inorganic platelet to enable assembly of prothrombinase complex and display an unusual zymogen (prothrombin) activation pattern. Inspired but not constrained by nature, it is of great interest to understand how FVa and FXa assembly on the inorganic surface (e.g., zeolites) and perform their biocatalytic function.

EXPERIMENTS

Given the important role of FVa C1-C2 domains in the assembly and activity of the prothrombinase complex, in this work, molecular dynamics simulations were performed to investigate the binding details of FVa A3-C1-C2 domains on the PS membranes and Ca²⁺-LTA-type (CaA) zeolite surface.

FINDINGS

We found that different from the natural PS membrane, FVa light chain repeatedly exhibits a strong C2 domain anchoring interaction on the CaA zeolite. It mainly arises from the porous surface structure of CaA zeolite and local highly dense solvation water clusters on the CaA zeolite surface restrict the movement of some lysine residues on the C2 domain. The anchoring interaction can be suppressed by reducing the surface negative charge density, so that FVa light chain can change from single-foot (only C2 domain) to double-foot (both C1-C2 domain) adsorption states on the zeolite surface. This double-foot adsorption state is similar to natural PS membrane systems, which may make FVa have higher cofactor activity.

Mild adsorption of carbon nitride (C3N3) nanosheet on a cellular membrane reveals its suitable biocompatibility

Recently, the novel hole-containing carbon nitride C₃N₃ nanomaterial was successfully synthesized, featuring outstanding and unique mechanical and electrical properties. However, to fully exploit this nanomaterial in biomedical applications, information regarding its biocompatibility is necessary. Herein, by using all-atom molecular dynamics simulations, we evaluate the interactions between a C₃N₃ nanosheet and a critical cellular component, that is, a lipid membrane bilayer. Our results indicate that the C₃N₃ nanosheet is able to interact with the lipid bilayer surface without affecting the membrane's structural integrity. Moreover, our results showed that the C₃N₃ nanosheet is adsorbed on the surface of the lipid bilayer without inflicting any structural damage to the membrane, regardless of the conditions of the system (that is, with and without restrains in the C₃N₃ nanosheet). Also, we found that both energy contributions, namely vdW and Coulomb energies, conjointly mediated the C₃N₃ adsorption process. In comparison and as expected, pristine graphene significantly disturbed the membrane structure. Perpendicularly-oriented-sheet simulations described the significance of the surface charges of the C₃N₃ nanosheet in prohibiting its insertion into the membrane. Detailed analysis indicated that the electrostatic attraction between the pores in the C₃N₃ structure and the lipid head amino groups stabilized the interaction restricting the insertion of the C₃N₃ structure deeper into the membrane. Our results suggested the importance of the negatively charged C₃N₃ pores when interacting with lipid membranes. Our findings shed light on the potential compatibility of C₃N₃ with biomembranes and its underlying molecular mechanism, which might provide a useful foundation for the future exploration of this 2D nanomaterial in biomedical applications.

Defect-Induced Double-Stranded DNA Unwinding on Graphene

Several works have shown that graphene materials can effectively regulate the double-stranded DNA (dsDNA) structures and are used to remove antibiotic resistance genes in the environment, during which the morphology of the graphene surface plays a key role. However, the mechanism of how different graphene surfaces interact with dsDNA is poorly documented. Here, the interactions of dsDNA with defective graphene (D-Gra) and pristine graphene (P-Gra) have been explored by molecular dynamics simulations. Our data clearly showed that both D-Gra and P-Gra were able to attract dsDNA to form stable bindings. However, the structure evolutions of dsDNA are distinctly different. In detail, D-Gra can initiate quick unwinding of dsDNA and cause significant structural disruption. While for P-Gra, it demonstrated a much weaker capability to disrupt the dsDNA structure. This difference is due to the strong electrostatic interaction between defects and DNA nucleotides. Nucleotides can be highly restricted by the defect while the other parts of dsDNA could move along the transverse directions of D-Gra. This effectively introduces a "pulling force" from the defect that causes the breaking of the hydrogen bonds between dsDNA base pairs. Such force finally leads to the serious unwinding of dsDNA. Our present findings could help us to better understand the molecular mechanism of how the dsDNA canonical B-form was lost upon adsorption to graphene. The findings of the key roles of defects on graphene are beneficial for the design of functional graphenic materials for biological and medical applications through nanostructure engineering.

Potential Unwinding of Double-Stranded DNA upon Binding to a Carbon Nitride Polyaniline (C3N) Nanosheet

Recently, carbon nitride polyaniline (C₃N) had attracted considerable attention from many scientific fields after its successful synthesis. However, thus far, limited efforts were devoted to reveal its potential effect to biomolecules, which correlated intimately with its further utilization. In this study, by using a molecular dynamics (MD) simulation approach, we investigated in detail the interaction between C₃N and a double-stranded DNA (dsDNA) segment to expose the underlying biological effect of C₃N to dsDNA and the corresponding molecular basis. MD simulation results demonstrated that dsDNA presented serious damages upon adsorption onto a C₃N nanosheet with the terminal base pairs denaturized, unwound, and directly packing on the C₃N surface, which implied that C₃N was potentially deleterious to biomolecules. This binding/unwinding process was mainly guided by a combination of van der Waals and π-π stacking interactions together with a continuous lateral migration of dsDNA. Moreover, the nanoscale dewetting also played an important role during the adsorption. These findings revealed the potential bio-effect of the C₃N nanomaterial and its molecular mechanism, which might benefit the future applications of C₃N-based nanostructures.

A first-principles study on the electronic and optical properties of a type-II C2N/g-ZnO van der Waals heterostructure

The structural, electronic and optical properties of a new van der Waals heterostructure, C2N/g-ZnO, composed of C2N and g-ZnO monolayers with an intrinsic type-II band alignment and a direct bandgap of 0.89 eV at the Γ point, are extensively studied using first-principles density functional theory calculations. The results indicate that the special optoelectronic properties of the constructed heterostructure mainly originate from the interlayer coupling and electron transfer between the C2N and g-ZnO monolayers, and the photogenerated electrons and holes are located on the C2N and g-ZnO layers, respectively, which reduces the recombination probability of the electron-hole pairs. According to Bader charge analysis, there are 0.029 electrons transferred from g-ZnO to C2N to form a built-in electric field of ∼9.5 eV at the interface. Furthermore, the tunability of the electronic properties of the C2N/g-ZnO heterostructure under vertical strain and electric field is explored. Under different strains, the type-II band alignment properties of the heterostructure are retained and the vertical compressive strain has a greater influence on the bandgap modulation than the vertical stretching strain. The implemented electric field also does not change the type-II band alignment but changes the bandgap of the heterostructure from 1.30 to 0.58 eV when the electric field strength varies from -0.6 to 0.6 V Å-1. In addition, the absorption spectrum of the C2N/g-ZnO heterostructure under solar light is also studied. The absorption range of the heterostructure varies from the ultraviolet to near-infrared region with the absorption intensity in the order of 105 cm-1. All of these studies indicate that the C2N/g-ZnO heterostructure has excellent electronic and optical properties and promising applications in nanoelectronics and optoelectronics.

Restricted binding of a model protein on C3N4 nanosheets suggests an adequate biocompatibility of the nanomaterial

The fixed binding pattern of protein adsorption to C₃N₄ plays a major role in the nanomaterial biocompatibility, which results from the inherent porous surface structure.

Exploring the effect of silicene monolayer on the structure and function of villin headpiece and amyloid fibrils by molecular dynamics simulations

With the development of various nanomaterial expected to be used in biomedical fields, it is more important to evaluate and understand their potential effects on biological system. In this work, two proteins with different structure, Villin Headpiece (HP35) with α-helix structure and protofibrils Aβ1-42 with five β-strand chains, were selected and their interactions with silicene were studied by means of molecular dynamics (MD) simulation to reveal the potential effect of silicene on the structure and function of biomolecules. The obtained results indicated that silicene could rapidly attract HP35 and Aβ1-42 fibrils onto the surface to form a stable binding. The adsorption strength was moderate and no significant structural distortion of HP35 and Aβ1-42 fibrils was observed. Moreover, the strength of calculated the H-bonds in neighbor chain of Aβ1-42 fibrils indicated that the mild interactions between silicene and fibrils could regularize the structure of Aβ1-42 fibrils and stabilize the interactions between five chains of fibrils protein, which might enhance the aggregation of Aβ1-42 fibrils. This study provides a new insight for understanding the interaction between nanomaterials and biomolecules and moves forward the development of silicene into biomedical fields.

C2N: A Class of Covalent Frameworks with Unique Properties

C2N is a unique member of the CnNm family (carbon nitrides), i.e., having a covalent structure that is ideally composed of carbon and nitrogen with only 33 mol% of nitrogen. C2N, with a stable composition, can easily be prepared using a number of precursors. Moreover, it is currently gaining extensive interest owing to its high polarity and good thermal and chemical stability, complementing carbon as well as classical carbon nitride (C3N4) in various applications, such as catalysis, environmental science, energy storage, and biotechnology. In this review, a comprehensive overview on C2N is provided; starting with its preparation methods, followed by a fundamental understanding of structure-property relationships, and finally introducing its application in gas sorption and separation technologies, as supercapacitor and battery electrodes, and in catalytic and biological processes. The review with an outlook on current research questions and future possibilities and extensions based on these material concepts is ended.

Tuning the binding behaviors of a protein YAP65WW domain on graphenic nano-sheets with boron or nitrogen atom doping

In recent years, nanomaterials have attracted considerable research attention for biological and medical related applications due to their well-recognized physical and chemical properties. However, the deep understanding of the binding process at the protein-nanomaterial interface is essential to solve the concern of nano-toxicity. Here, we study the interactions between the recently reported graphenic nano-sheets, BC3 and C3N, and a prototypical protein (YAP65WW domain) via atomistic molecular dynamics simulations. Our simulations reveal that elemental doping is an effective way to tune the binding characteristics of YAP65WW with two nanomaterials. While YAP65WW can be attracted by two nanomaterials, the BC3 sheet is less able to disrupt the protein structure than C3N. From the energy point of view, this is because protein residues demonstrate a binding preference with the trend from electron rich nitrogen to electron deficient boron. Structural analyses of the bio-nano interface revealed the formation of an ordered water shell on the BC3 surface, which was compatible to the crystal pattern of BC3. When a protein binds with BC3, these interfacial water molecules protect the protein from being disrupted. We suggest that elemental doping is efficient to produce fruitful biological-effects of graphenic nanomaterials, which make it a prospective solution for the future design and fabrication of advanced nanomaterials with desired function.

Controlling ion transport in a C2N-based nanochannel with tunable interlayer spacing

Selective ion transport through a nanochannel formed by stacked two-dimensional materials plays a key role in water desalination, nanofiltration, and ion separation. Although there have been many functional nanomaterials used in these applications, how to well control ion transport in a laminar structure so as to obtain the desired selectivity still remains a challenging problem. In the present work, the transport of ions through a C₂N-based nanochannel is investigated by using all-atom molecular dynamics simulation. It is found that C₂N-based nanochannels with different interlayer spacing posses diverse ion selectivity, which is mainly attributed to the distinct loading capability among ions and the different velocity of ions inside the nanochannel. Moreover, we also find that the ion selectivity is dependent on the electric field, but nearly independent of the salt concentration. The present study may provide some physical insights into the experimental design of C₂N-based nanodevices in nanofiltration.

pH-Dependent adsorption of aromatic compounds on graphene oxide: An experimental, molecular dynamics simulation and density functional theory investigation

This work provides a comprehensive understanding for the pH-dependent adsorption of aromatic compounds (ACs) on graphene oxide (GO). Isothermal and kinetics experiments indicated both adsorption capacity and adsorption rate were suppressed at higher pH, and the mechanisms were revealed by molecular dynamics simulations and density functional theory calculations. More specifically, π-π, hydrogen bond, vdWs, and water-mediated steric hindrance interactions were examined to reveal how pH affected the adsorption capacity, and microscopic dynamic adsorption process was captured to reveal how pH affected the adsorption rate. Results showed the reduced adsorption capacity at higher pH was mediated by increased electrostatic repulsion, weakened π-π interaction, and increased water-mediated steric hindrance. The pH-dependent behaviour of GO was responsible for the effect of pH on adsorption rate. Self-aggregation of GO at lower pH helped to capture ACs and created more favourable adsorption sites. Upon the adsorption of ACs on GO, GO/water/AC/water/GO sandwich-like structure formed, which was also mediated by solution pH. Overall, pH affects the adsorption of ACs on GO by regulating driving forces, adsorption process, and the configuration property of GOAC complex.

Delicate Balance of Non-Covalent Forces Govern the Biocompatibility of Graphitic Carbon Nitride towards Genetic Materials

Despite a plethora of suggested technological and biomedical applications, the nanotoxicity of two-dimensional (2D) graphitic carbon nitride (g-C₃ N₄ ) towards biomolecules remains elusive. To address this issue, we employ all-atom classical molecular dynamics simulations and investigate the interactions between nucleic acids and g-C₃ N₄ . It is revealed that, toxicity is modulated through a subtle balance between electrostatic and van der Waals interactions. When the exposed nucleobases interact through predominantly short-ranged van der Waals and π-π stacking interactions, they get deviated from their native disposition and adsorb on the surface, leading to loss of self-stacking and intra-quartet H-bonding along with partial disruption of the native structure. In contrast, for the interaction with double-stranded structures of both DNA and RNA, long-range electrostatics govern the adsorption phenomena since the constituent nucleobases are relatively concealed and wrapped, thereby resulting in almost complete preservation of the nucleic acid structures. Construction of free energy landscapes for lateral translation of adsorbed nucleic acids suggests decent targeting specificity owing to their restricted movement on g-C₃ N₄ . The release times of nucleic acids adsorbed through predominant electrostatics are significantly less than those adsorbed through stacking with the surface. It is therefore proposed that g-C₃ N₄ would induce toxicity towards any biomolecule having bare residues available for strong van der Waals and π-π stacking interactions relative to those predominantly interacting through electrostatics.

Binding patterns and dynamics of double-stranded DNA on the phosphorene surface

Phosphorene, a monolayer of black phosphorus, has emerged as one of the most promising two-dimensional (2D) nanomaterials for various applications in the post-graphene-discovery period due to its highly anisotropic structure and novel properties. In order to apply phosphorene in biomedical fields, it is crucial to understand how it interacts with biomolecules. Herein, we use both molecular dynamics (MD) simulations and experimental techniques to investigate the interactions of phosphorene with a dsDNA segment. Our results reveal that dsDNA can form a stable binding on the phosphorene surface through the terminal base pairs and adopt an upright orientation regardless of its initial configurations. Moreover, the binding strength of dsDNA with phosphorene is found to be mild and does not cause significant distortion in the internal structure of dsDNA. This phenomenon is attributed to the weaker dispersion interaction between dsDNA and phosphorene. Further analysis of the free energy profile calculated by the umbrella sampling technique suggests that the puckered surface morphology significantly reduces the adsorption free energy of DNA bases to phosphorene. Compared to graphene, phosphorene is found to show a milder attraction to DNA, which is confirmed by our electrophoresis experiments. We believe that these findings provide valuable insight into the molecular interactions between phosphorene and dsDNA which may prompt further investigation of phosphorene for future biomedical applications.

Anisotropic protein diffusion on nanosurface

The unique puckered structure of α-phase phosphorene carbide (α-PC) results in anisotropic electronic and thermal transporting properties. In the present work, the interactions between a model protein, villin headpiece sub-domain (HP35), and the surface of α-PC and monolayer black phosphorus (MBP, another puckered nanostructure) were explored by molecular dynamic (MD) simulations. It is found that HP35 diffuses quickly only along the zigzag direction of the α-PC surface. On the MBP surface, HP35 migrates mainly along the zigzag direction but can also easily stride over the ridges and grooves along the armchair direction. Moreover, the mild binding strength between α-PC and HP35 does not cause distortion in the protein structure. The intrinsic biocompatibility of α-PC, which is distinct from several other widely studied nanomaterials, such as carbon nanotubes, graphene and MoS2, makes it a promising candidate in functional biomedical applications.

Orientational DNA binding and directed transport on nanomaterial heterojunctions

A deep understanding of the interactions between nanomaterials and biomolecules is critical for biomedical applications of nanomaterials. In this paper, we study the binding patterns, structural stabilities and diffusions of a double stranded DNA (dsDNA) segment on two recently reported graphene derivatives, boronic graphene (BC3) and nitrogenized graphene (C3N), with molecular dynamics (MD) simulations. Our results demonstrate that dsDNA exhibits a highly favored binding mode with an upright orientation on BC3 and C3N, independent of the initial configurations. In contrast to graphene (GRA) which demonstrates a cytotoxic feature, BC3 and C3N show high biocompatibility without causing evident structural distortions to the dsDNA duplex, benefitting from the periodic atomic charge distributions. Most interestingly, highly directional dsDNA transport is realized by formation of BC3/GRA and C3N/GRA in-plane heterojunctions, where the dsDNA migrating direction is uniformly BC3 → GRA → C3N. Furthermore, free energy profiling calculated by the umbrella sampling technique quantitatively supports these observations. Insights from our study would potentiate and guide future studies of graphenic 2D materials and bring about a flourishing new branch of in-plane heterojunction applications as targeted drug delivery templates in biomedical research.

Screening two dimensional materials for the transportation and delivery of diverse genetic materials

In spite of several reports of graphene and other 2D materials concerning their capacity for biomolecular adsorption and delivery, recent toxicity evaluations found them to be nanotoxic toward different biomolecules, especially nucleic acids. Therefore, there is urgent demand for the synthesis of 2D materials exhibiting biocompatible and non-nanotoxic features. In this article, employing classical molecular dynamics simulations, we provide a benchmarking of h2D-C2N, graphene and hexagonal boron nitride (h-BN) toward the adsorption, preservation, targeting and delivery of various classes of nucleic acids namely single stranded DNA, double stranded natural as well as unnatural base substituted DNA and two different types of human telomeric guanine quadruplexes, all comprising different secondary structures. Our simulations reveal that, while h2D-C2N preserves the structures of most of the nucleic acids, graphene and h-BN disrupt them through strong π-π stacking with aromatic nucleobases. Interestingly, for the first time we identified a 'quartet-by-quartet' disruption mechanism of guanine quadruplexes, but only on graphene and h-BN. The lateral diffusion of adsorbed nucleic acids over C2N is restricted unlike that over both graphene and h-BN, thereby increasing the targeting efficacy for C2N. Modeling of the delivery phenomena suggests orders of magnitude longer release times from graphene and h-BN compared to C2N, thereby demonstrating the preferential suitability of C2N for all the hierarchical steps of nucleic acid transportation.

Mild lipid extraction and anisotropic cell membrane penetration of α-phase phosphorene carbide nanoribbons by molecular dynamics simulation studies

α-PC penetrates the interior of membrane efficiently only along its zigzag direction rather than its armchair direction.

Stimulating antibacterial activities of graphitic carbon nitride nanosheets with plasma treatment

As a widely studied photoactive antibacterial nanomaterial, the intrinsic antibacterial traits of graphitic carbon nitride (g-C3N4) as a two-dimensional nanomaterial have not been reported so far. Herein, nitrogen-plasma-treated g-C3N4 (N-g-C3N4) nanosheets and their influence on bactericidal characteristics are investigated. Bactericidal rates of more than 99% have been successfully achieved for 8 kinds of foodborne pathogenic bacteria by N-g-C3N4 with 8 h incubation in the dark. The achieved rates are percentage wise 10 times higher than those for pristine g-C3N4. Cell rupture caused by direct mechanical contact between g-C3N4 nanosheets and cell membranes is observed. X-ray photoelectron spectroscopy revealed a substantial loss of surface defects and nitrogen vacancies in N-g-C3N4. Molecular dynamics simulations further indicated that the largely sealed defects of N-g-C3N4 enhanced the electrostatic attraction between inherent pores and lipid heads; thus, further insertion of N-g-C3N4 was promoted, resulting in enhanced antibacterial activity. This study establishes novel fabrication and application strategies for carbon based antibacterial nanomaterials.

Cytotoxicity of C2N Originating from Oxidative Stress Instead of Membrane Stress

Two-dimensional (2D) nanomaterials have shown promising potential in a wide range of biomedical applications. Nevertheless, the rapid advances in this field recently have also evoked growing concerns about their toxic effects on humans and the environment. Herein, we systematically investigate the potential cytotoxicity of C₂N nanosheets, a newly emerging 2D nitrogenized graphene with uniform holes in the basal plane. Our in vitro experiments show that C₂N is toxic to human umbilical vein/vascular endothelium cells. The further combined experimental and theoretical studies unravel that the cytotoxicity of C₂N mainly originates from its oxidative capability toward the antioxidant molecules, leading to excessive accumulation of reactive oxygen species in cells. Compared with graphene oxide, C₂N exerts a relatively milder cytotoxicity, and importantly, this novel material shows negligible physical destruction effects on cell membranes, suggesting that C₂N might be a potential alternative to graphene and its derivatives in biomedical research. This work sheds light on the cytotoxicity of C₂N nanosheets and the underlying mechanism, which is crucial for the future utilization of this 2D nanomaterial in related biomedical fields.

Potential blockade of the human voltage-dependent anion channel by MoS2 nanoflakes

Despite significant interest in molybdenum disulfide (MoS2) nanomaterials, particularly in biomedicine, their biological effects have been understudied. Here, we explored the effect of MoS2 nanoflakes on the ubiquitous mitochondrial porin voltage-dependent anion channel (VDAC1), using a combined computational and functional approach. All-atomic molecular dynamics simulations suggest that MoS2 nanoflakes make specific contact interactions with human VDAC1. We show that the initial contacts between hVDAC1 and the nanoflake are hydrophobic but are subsequently enhanced by a complex interplay of van der Waals (vdW), hydrophobic and electrostatic interactions in the equilibrium state. Moreover, the MoS2 nanoflake can insert into the lumen of the hVDAC1 pore. Free-energy calculations computed by the potential of mean force (PMF) verify that the blocked configuration of the MoS2-hVDAC1 complex is more energetically favorable than the non-blocked binding mode. Consistent with these predictions, we showed that MoS2 depolarizes the mitochondrial membrane potential (Ψm) and causes a decrease in the viability of mammalian tissue culture cells. These findings might shed new light on the potential biological effect of MoS2 nanomaterials.

Superior Compatibility of C2 N with Human Red Blood Cell Membranes and the Underlying Mechanism

The widespread use of nanomaterials, such as carbon based 2D nanomaterials, in biomedical applications, has been accompanied by a growing concern on their biocompatibility, and in particular, on how they may affect the integrity of cell membranes. Herein, the interactions between C₂ N, a novel 2D nanomaterial, and human red blood cell membranes are explored using a combined experimental and theoretical approach. The experimental microscopies show that C₂ N exerts a negligible hemolysis effect on the blood cells with a superior compatibility to their cell membranes, when compared with the control system, reduced graphene oxide (rGO), which is found to be highly hemolytic. The molecular dynamics simulations further reveal the underlying molecular mechanisms, which indicate that C₂ N prefers to be adsorbed flat on the water-membrane interface. Interaction energy analyses demonstrate the crucial role of Coulombic contributions, originating from the unique electrostatic potential surface of C₂ N, in preventing C₂ N from penetrating into cell membranes. These findings indicate a high compatibility of C₂ N with cell membranes, which may provide useful foundation for the future exploration of this 2D nanomaterial in related biomedical applications.

Wrinkle- and Edge-Adsorption of Aromatic Compounds on Graphene Oxide as Revealed by Atomic Force Microscopy, Molecular Dynamics Simulation, and Density Functional Theory

In this work, the favorable adsorption sites of aromatic compounds (ACs) on graphene oxide (GO) are characterized with both experimental and theoretical approaches. The results show that ACs exhibit a strong preference in adsorbing near the wrinkles and edges. Further analyses reveal that the edge-adsorption is mainly guided by the stronger π-π interaction near edges, accompanied by a stronger hydrogen bond interaction between carboxyl groups and ACs. Additionally, the water-mediated steric hindrance and flexibility of carboxyl groups also contribute to the edge-adsorption. A higher density of atoms and electrons is the main mechanism for the wrinkle-adsorption, and structural investigations indicate that the roughness serving as a steric hindrance for the ACs migration also contributes to the wrinkle-adsorption. This wrinkle- and edge-adsorption pattern will shed light on the design of GO-related environmental materials.

Gauging the Nanotoxicity of h2D-C2N toward Single-Stranded DNA: An in Silico Molecular Simulation Approach

Recent toxicological assessments of graphene, graphene oxides, and some other two-dimensional (2D) materials have shown them to be substantially toxic at the nanoscale, where they inhibit and eventually disrupt biological processes. These shortfalls of graphene and analogs have resulted in a quest for novel biocompatible 2D materials with minimum cytotoxicity. In this article, we demonstrate C₂N (h2D-C₂N), a newly synthesized 2D porous graphene analog, to be non-nanotoxic toward genetic materials from an "in-silico" point of view through sequence-dependent binding of different polynucleotide single-stranded DNA (ssDNA) onto it. The calculated binding energy of nucleobases and the free energy of binding of polynucleotides follow the common trait, cytosine > guanine > adenine > thymine, and are well within the limits of physisorption. Ab-initio simulations completely exclude the possibility of any chemical reaction, demonstrating purely noncovalent binding of nucleobases with C₂N through a crucial interplay between hydrogen bonding and π-stacking interactions with the surface. Further, we show that the extent of distortion inflicted upon ssDNA by C₂N is negligible. Analysis of the density of states of the nucleobase-C₂N hybrids confirms minimum electronic perturbation of the bases after adsorption. Most importantly, we demonstrate the potency of C₂N in nucleic acid transportation via reversible binding of ssDNA. The plausible use of C₂N as a template for DNA repair is illustrated through an example of C₂N-assisted complementary ssDNA winding.

Ion transport through a nanoporous C2N membrane: the effect of electric field and layer number

Using all-atom molecular dynamic simulations, we show that a monolayer C₂N membrane possesses higher permeability and excellent ion selectivity, and that multilayer C₂N membranes have promising potential for water desalination.

Egg-shell derived carbon dots for base pair selective DNA binding and recognition

Here, we have used food waste derived chicken egg shell membrane as a cost effective carbon source for the synthesis of heteroatom doped fluorescent carbon dots. We are able to apply these synthesized carbon dots as a new fluorescent probe for label free base pair selective and sequence specific double stranded DNA binding.