Amino acid analogues bind to carbon nanotube via π-π interactions: Comparison of molecular mechanical and quantum mechanical calculations

Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene

There is still growing interest in graphene interactions with proteins, both for its possible biological applications and due to concerns over detrimental effects at the cellular level. As with any process involving proteins, an understanding of amino acid composition is desirable. In this work, we systematically studied the adsorption process of amino acids onto pristine graphene via rigorous free-energy calculations. We characterized the free energy, potential energy, and entropy of the adsorption of all proteinogenic amino acids. The energetic components were further separated into pair interaction contributions. A linear correlation was found between the free energy and the solvent accessible surface area change during adsorption (ΔSASAads) over pristine graphene and uncharged amino acids. Free energies over pristine graphene were compared with adsorption onto graphene oxide, finding an almost complete loss of the favorability of amino acid adsorption onto graphene. Finally, the correlation with ΔSASAads was used to successfully predict the free energy of adsorption of several penta-l-peptides in different structural states and sequences. Due to the relative ease of calculating the ΔSASAads compared to free-energy calculations, it could prove to be a cost-effective predictor of the free energy of adsorption for proteins onto nonpolar surfaces.

Investigating the Stacking Interactions Responsible for Driving 3D Self-Association of Tricarb Macrocycles

We have investigated the noncovalent forces that play a crucial role in the three-dimensional (3D) self-association of the tricarb macrocycle (composed of alternating triazoles and carbazoles) to understand the multilayer stacks observed through electron microscopy. To explore this idea quantitatively, we have investigated a stacked dimer model of tricarb, where we consider homochiral as well as heterochiral forms of the dimer. We have computed the rotational potential energy surface of the dimer by conducting an angle-dependent scan between the two macrocycles using different levels of theory including the RI-MP2 ab initio method. We observe that dimers oriented at an angle of 60° exhibit the highest stability, while a secondary minimum is observed at an angle of 30°. While density functional theory (DFT) describes the behavior of both minima very close to that obtained with RI-MP2, semiempirical and MM models appear to obtain only a shoulder instead of the second minimum. To further understand the underlying interactions responsible for stabilizing the self-assembly of the macrocycles, we employed energy decomposition analysis (EDA) using SAPT0. This quantitative assessment allowed us to identify the major contributing noncovalent interactions, including electrostatic, exchange-repulsion, dispersion, and induction. Finally, we expanded our study to evaluate the accuracy of the MIM (molecules-in-molecules) fragmentation methodology in capturing the crucial π-stacking interactions. Our benchmarking results using the MIM method accurately replicated the angle-dependent PES results. This shows the efficacy of MIM in predicting the noncovalent interactions responsible for the construction of 3D and other higher-order nanoarchitectures for tricarb and related compounds.

Molecular Dynamics Study of the Curvature-Driven Interactions between Carbon-Based Nanoparticles and Amino Acids

We researched the interaction between six representative carbon-based nanoparticles (CBNs) and 20 standard amino acids through all-atom molecular dynamics simulations. The six carbon-based nanoparticles are fullerene(C60), CNT55L3, CNT1010L3, CNT1515L3, CNT2020L3, and two-dimensional graphene (graphene33). Their curvatures decrease sequentially, and all of the CNTs are single-walled carbon nanotubes. We observed that as the curvature of CBNs decreases, the adsorption effect of the 20 amino acids with them has an increasing trend. In addition, we also used multi-dimensional clustering to analyze the adsorption effects of 20 amino acids on six carbon-based nanoparticles. We observed that the π-π interaction still plays an extremely important role in the adsorption of amino acids on carbon-based nanoparticles. Individual long-chain amino acids and "Benzene-like" Pro also have a strong adsorption effect on carbon-based nanoparticles.

Ionic Liquid Decelerates Single-Stranded DNA Transport through Molybdenum Disulfide Nanopores

Nanopores in two-dimensional (2D) materials have emerged to offer in principle necessary spatial resolution for high-throughput DNA sequencing. However, their fidelity is severely limited by the fast DNA translocation. A recent experiment indicates that introducing ionic liquids could slow down DNA translocation in a MoS₂ nanopore. However, the corresponding in-depth molecular mechanism underlying the experimental findings is not fully understood, which is crucial for the future improvement of rational DNA translocation control. Here, we computationally investigate and then experimentally identify the effect of BmimCl ionic liquid on the retardation of ssDNA translocation through a single-layer MoS₂ nanopore. Our all-atom molecular dynamics simulations demonstrate that the strong interaction between Bmim⁺ and ssDNA offers a considerable dragging force to decelerate the electrophoretic motion of ssDNA in the BmimCl solution. Moreover, we show that Bmim⁺ ions exhibit preferential binding on the sulfur edges of the nanopore. These Bmim⁺ in the pore region can not only act as a steric blockage but also form π-π stackings with nucleobases, which provide a further restriction on the ssDNA motion. Therefore, our molecular dynamics simulation investigations deepen the understanding of the critical role of ionic liquid in DNA translocation through a nanopore from a molecular landscape, which may benefit practical implementations of ionic liquids in nanopore sequencing.

Shedding light on the binding mechanism of kinase inhibitors BI-2536, Volasetib and Ro-3280 with their pharmacological target PLK1

In the present work, the interactions of the novel kinase inhibitors BI-2536, Volasetib (BI-6727) and Ro-3280 with the pharmacological target PLK1 have been studied by fluorescence spectroscopy and molecular dynamics calculations. High Stern-Volmer constants were found in fluorescence experiments suggesting the formation of stable protein-ligand complexes. In addition, it was observed that the binding constant between BI-2536 and PLK1 increases about 100-fold in presence of the phosphopeptide Cdc25C-p that docks to the polo box domain of the protein and releases the kinase domain. All the determined binding constants are higher for the kinase inhibitors than for their competitor for the active center (ATP) being BI-2536 and Volasertib the inhibitors that showed more affinity for PLK1. Calculated binding free energies confirmed the higher affinity of PLK1 for BI-2536 and Volasertib than for ATP. The higher affinity of the inhibitors to PLK1 compared to ATP was mainly attributed to stronger van der Waals interactions. Results may help with the challenge of designing and developing new kinase inhibitors more effective in clinical cancer therapy.

Structural, dynamic, and hydration properties of quercetin and its aggregates in solution

Quercetin is a flavonoid present in the human diet with multiple health benefits. Quercetin solutions are inhomogeneous even at very low concentrations due to quercetin's tendency to aggregate. We simulate, using molecular dynamics, three systems of quercetin solutions: infinite dilution, 0.22 M, and 0.46 M. The systems at the two highest concentrations represent regions of the quercetin aggregates, in which the concentration of this molecule is unusually high. We study the behavior of this molecule, its aggregates, and the modifications in the surrounding water. In the first three successive layers of quercetin hydration, the density of water and the hydrogen bonds formations between water molecules are smaller than that of bulk. Quercetin has a hydrophilic surface region that preferentially establishes donor hydrogen bonds with water molecules with relative frequencies from 0.12 to 0.46 at infinite dilution. Also, it has two hydrophobic regions above and below the planes of its rings, whose first hydration layers are further out from quercetin (≈0.3 Å) and their water molecules do not establish hydrogen bonds with it. Water density around the hydrophobic regions is smaller than that of the hydrophilic. Quercetin molecules aggregate inπ-stacking configurations, with a distance of ≈0.37 nm between the planes of their rings, and form bonds between their hydroxyl groups. The formation of quercetin aggregates decreases the hydrogen bonds between quercetin and the surrounding water and produces a subdiffusive behavior in water molecules. Quercetin has a subdiffusive behavior even at infinite dilution, which increases with the number of molecules within the aggregates and the time they remain within them.

Molecular Alignment of a Meta-Aramid on Carbon Nanotubes by In Situ Interfacial Polymerization

Molecularly organized nanocomposites of polymers and carbon nanotubes (CNTs) have great promise as high-performance materials; in particular, conformal deposition of polymers can control interfacial properties for mechanical load transfer, electrical or thermal transport, or electro/chemical transduction. However, controllability of polymer-CNT interaction remains a challenge with common processing methods that combine CNTs and polymers in melt or in solution, often leading to nonuniform polymer distribution and CNT aggregation. Here, we demonstrate CNTs within net-shape sheets can be controllably coated with a conformal coating of meta-aramid by simultaneous capillary infiltration and interfacial polymerization. We determine that π-interaction between the polymer and CNTs results in chain alignment parallel to the CNT outer wall. Subsequent nucleation and growth of the precipitated aramid forms a smooth continuous layered sheath around the CNTs. These findings motivate future investigation of mechanical properties of the resulting composites, and adaptation of the in situ polymerization method to other substrates.

Extreme Dynamic Performance of Nanofiber Mats under Supersonic Impacts Mediated by Interfacial Hydrogen Bonds

Achieving extreme dynamic performance in nanofibrous materials requires synergistic exploitation of intrinsic nanofiber properties and inter-fiber interactions. Regardless of the superior intrinsic stiffness and strength of carbon nanotubes (CNTs), the weak nature of van der Waals interactions limits the CNT mats from achieving greater performance. We present an efficient approach to augment the inter-fiber interactions by introducing aramid nanofiber (ANF) links between CNTs, which forms stronger and reconfigurable interfacial hydrogen bonds and π-π stacking interactions, leading to synergistic performance improvement with failure retardation. Under supersonic impacts, strengthened interactions in CNT mats enhance their specific energy absorption up to 3.6 MJ/kg, which outperforms widely used bulk Kevlar-fiber-based protective materials. The distinct response time scales of hydrogen bond breaking and reformation at ultrahigh-strain-rate (∼10⁷-10⁸ s^-1) deformations additionally manifest a strain-rate-dependent dynamic performance enhancement. Our findings show the potential of nanofiber mats augmented with interfacial dynamic bonds─such as the hydrogen bonds─as low-density structural materials with superior specific properties and high-temperature stability for extreme engineering applications.

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.

Carbon nanocarriers deliver siRNA to intact plant cells for efficient gene knockdown

Posttranscriptional gene silencing (PTGS) is a powerful tool to understand and control plant metabolic pathways, which is central to plant biotechnology. PTGS is commonly accomplished through delivery of small interfering RNA (siRNA) into cells. Standard plant siRNA delivery methods (Agrobacterium and viruses) involve coding siRNA into DNA vectors and are only tractable for certain plant species. Here, we develop a nanotube-based platform for direct delivery of siRNA and show high silencing efficiency in intact plant cells. We demonstrate that nanotubes successfully deliver siRNA and silence endogenous genes, owing to effective intracellular delivery and nanotube-induced protection of siRNA from nuclease degradation. This study establishes that nanotubes could enable a myriad of plant biotechnology applications that rely on RNA delivery to intact cells.

Two-Dimensional (2D) Covalent Organic Framework as Efficient Cathode for Binder-free Lithium-Ion Battery

Searching new organic cathode materials to address the issues of poor cycle stability and low capacity in lithium ion batteries (LIBs) is very important and highly desirable. In this research, a 2D boroxine-linked chemically-active pyrene-4,5,9,10-tetraone (PTO) covalent organic framework (2D PPTODB COFs) was synthesized as an organic cathode material with remarkable electrochemical properties, including high electrochemical activity (four redox electrons), safe oxidation potential window (between 2.3 and 3.08 V vs. Li/Li⁺ ), superb structural/chemical stability, and strong adhesiveness. A binder-free cathode was obtained by mixing 70 wt % PPTODB and 30 wt % carbon nanotubes (CNTs) as a conductive additive. Promoted by the fast kinetics of electrons/ions, high electrochemical activity, and effective π-π interaction between PPTODB and CNTs, LIBs with the as-prepared cathode exhibited excellent electrochemical performance: a high specific capacity of 198 mAh g^-1 , a superb rate ability (the capacity at 1000 mA g^-1 can reach 76 % of the corresponding value at 100 mA g^-1 ), and a stable coulombic efficiency (≈99.6 % at the 150th cycle). This work suggests that the concept of binder-free 2D electroactive materials could be a promising strategy to approach energy storage with high energy density.

Molecular dynamics study on the encapsulation and release of anti-cancer drug doxorubicin by chitosan

Doxorubicin (DOX) is a broad-spectrum anti-tumor drug, but it has certain limitations in its therapeutic effects due to poor tumor selectivity. Chitosan-based pH-sensitive polymers drug delivery systems could improve DOX's activity and selectivity against tumor cells. Understanding the atomic interaction mechanism between chitosan and DOX at different pH levels is important in the design and application of chitosan-based drug delivery systems. In this study, molecular dynamics simulations were performed to investigate the encapsulation and release of DOX by chitosan at different pH levels. Our results show that the protonation state of amine groups of chitosan and the π-π stacking interaction between the conjugated anthraquinone ring of DOX regulate the interaction behavior between chitosan and DOX. Moreover, DOX could gradually release from chitosan at acidic pH environment in tumor tissue. These results revealed the underlying atomic interaction mechanism between DOX and chitosan at various pH levels and may provide novel ideas for the design and application of chitosan-based drug delivery system.

Structural and theoretical study of four novel norcantharidine derivatives: two new cases of conditional isomorphism

Structural and theoretical studies of four novel 5,6-dehydronorcantharidine (DNCA)/norcantharidine (NCA) derivatives, namely (3aR,4S,7R,7aS)-2-phenyl-3a,4,7,7a-tetrahydro-4,7-epoxy-1H-isoindole-1,3(2H)-dione, C₁₄H₁₁NO₃ (DNCA-A), (3aR,4S,7R,7aS)-2-(4-nitrophenyl)-3a,4,7,7a-tetrahydro-4,7-epoxy-1H-isoindole-1,3(2H)-dione, C₁₄H₁₀N₂O₅ (DNCA-NA), (3aR,4S,7R,7aS)-2-(4-nitrophenyl)-3a,4,5,6,7,7a-hexahydro-1H-4,7-epoxyisoindole-1,3(2H)-dione, C₁₄H₁₂N₂O₅ (NCA-NA), and (3aR,4S,7R,7aS)-2-(2-hydroxyethyl)-3a,4,5,6,7,7a-hexahydro-1H-4,7-epoxyisoindole-1,3(2H)-dione, C₁₀H₁₃NO₄ (NCA-AE), are reported. The supramolecular interactions and single-crystal structural characteristics of these molecules, together with the crystal structures of four other similar molecules, i.e. NCA-A (the 4-phenyl derivative of NCA-NA), DNCA-AE (the 5,6-unsaturated derivative of NCA-AE), DNCA and NCA, were analysed. Surprisingly, DNCA-A and NCA-A, as well as DNCA-NA and NCA-NA, proved to be isomorphic, while DNCA-AE and NCA-AE, as well as DNCA and NCA, have very different crystal structures. These are very rare isostructural examples between unsaturated and saturated oxanorbornene/oxanorbornane derivatives. To further explore how noncovalent interactions (NCIs) affect the degree of isomorphism in this particular series of rigid molecules where there is a fairly limited conformational degree of freedom, all four pairs of crystal structures were analyzed in parallel. The differentiation in NCIs which entails the packing mode of similar molecules is supported by energy calculations based on real or exchanged crystal structures. Our results show that minor structural differences may result in very different supramolecular interactions, and so lead to altered packing modes in the crystalline solids. Even if isostructurality sometimes occurs, the possibility of various molecular packing types cannot be ruled out. On the other hand, isomorphism may just be the result of kinetic possibilities instead of relative thermodynamic stabilities. Though crystal structure prediction is formidable, the comparison method based on existing crystal structures and quantum calculations can be used to predict the probability of isomorphism. This understanding will help us to design new norbornene derivatives with specified structures.

A review on peptide functionalized graphene derivatives as nanotools for biosensing

Peptides exhibit unique binding behavior with graphene and its derivatives by forming bonds on its edges and planes. This makes them useful for sensing and imaging applications. This review with (155 refs.) summarizes the advances made in the last decade in the field of peptide-GO bioconjugation, and the use of these conjugates in analytical sciences and imaging. The introduction emphasizes the need for understanding the biotic-abiotic interactions in order to construct controllable peptide-functionalized graphitic material-based nanotools. The next section covers covalent and non-covalent interactions between peptide and oxidized graphene derivatives along with a discussion of the adsorption events during interfacing. We then describe applications of peptide-graphene conjugates in bioassays, with subsections on (a) detection of cancer cells, (b) monitoring protease activity, (c) determination of environmental pollutants and (d) determination of pathogenic microorganisms. The concluding section describes the current status of peptide functionalized graphitic bioconjugates and addresses future perspectives. Graphical abstractSchematic representation depicting biosensing applications of peptide functionalized graphene oxide.

Spontaneous ssDNA stretching on graphene and hexagonal boron nitride in plane heterostructures

Single-stranded DNA (ssDNA) molecules in solution typically form coiled structures, therefore stretching ssDNA is extremely crucial before applying any nanotechnology for ssDNA analysis. Recent advances in material fabrication enable the deployment of nanochannels to manipulate, stretch, sort and map double-stranded DNA (dsDNA) molecules, however nanochannels fail to stretch ssDNA molecules due to the ultra-short persistence length and the potential nonspecific-interaction-induced clogging. Given the significance of ssDNA stretching in genome analysis, here we report an ssDNA stretching platform: two dimensional in-plane heterostructure comprising graphene and hexagonal boron nitride (h-BN), and show that ssDNA can be stretched on a h-BN nanostripe sandwiched between two adjacent graphene domains (“nanochannel”). We further show that with a biasing voltage the stretched ssDNA can be electrophoretically transported along the “nanochannel”, allowing easy controls/manipulations. When being conveniently integrated with existing atomic resolution sensors, the heterostructure platform paves the way for sequencing DNA on a planar surface.

Single stranded DNA analysis is of interest for a range of applications; however, natural folding of DNA can cause problems with this. Here, the authors report on the in silico analysis of graphene and hexagonal-boron-nitride structures for the stretching and unfolding of DNA to allow for analysis.

Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications

Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.

A New Heterogeneous Catalyst Obtained via Supramolecular Decoration of Graphene with a Pd2+ Azamacrocyclic Complex

A new G-(H2L)-Pd heterogeneous catalyst has been prepared via a self-assembly process consisting in the spontaneous adsorption, in water at room temperature, of a macrocyclic H2L ligand on graphene (G) (G + H2L = G-(H2L)), followed by decoration of the macrocycle with Pd2+ ions (G-(H2L) + Pd2+ = G-(H2L)-Pd) under the same mild conditions. This supramolecular approach is a sustainable (green) procedure that preserves the special characteristics of graphene and furnishes an efficient catalyst for the Cu-free Sonogashira cross coupling reaction between iodobenzene and phenylacetylene. Indeed, G-(H2L)-Pd shows an excellent conversion (90%) of reactants into diphenylacetylene under mild conditions (50 °C, water, aerobic atmosphere, 14 h). The catalyst proved to be reusable for at least four cycles, although decreasing yields down to 50% were observed.

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

Facet-regulated adhesion of double-stranded DNA on palladium surfaces

A better understanding of interactions between metal-nanomaterial surfaces and biomolecules such as DNAs is critical for their biomedical applications. Here we investigated double-stranded DNA (dsDNA) adhering to palladium (Pd) nanosheets with two different exposed facets, {100} and {111}, using a combined computational and experimental approach. Different dsDNA binding modes on the two surfaces were observed, with a surprising "upright" conformation on Pd(100) and a "flat" conformation on Pd(111). Molecular dynamics simulations showed a stronger binding of the dsDNA on Pd(111) than Pd(100), which resulted in significant conformational changes and hydrogen bond breakage in the dsDNA on Pd(111). Further analyses revealed that the different binding strengths were caused by the number and arrangement of water molecules in the first solvation shell (FSS) of the two Pd surfaces. The water hydrogen bond network in the FSS of Pd(100) is compact and resists the embedding of dsDNA, while it is less compact on Pd(111), which allows penetration of dsDNA and its direct contact with Pd(111) surface atoms, thereby exhibiting stronger binding. Further free energy calculations with umbrella sampling supported these observations. Finally, these computational predictions on the adsorption capacity of dsDNA on Pd surfaces were confirmed by gel electrophoresis experiments.

The Photothermal Effect of Targeted Methotrexate-Functionalized Multi-Walled Carbon Nanotubes on MCF7 Cells

Our goal is to reduce the release rate of methotrexate (MTX) and increase cell death efficiency.Carboxylated multi-walled carbon nanotubes (MWCNT-COOH) were functionalized with MTX as a cytotoxic agent, FA as a targeting moiety and polyethylene amine (PEI) as a hydrophilic agent. Ultimately, MWCNT-MTX and MWCNT-MTX-PEI-FA were synthesized. Methotrexate release studies were conducted in PBS and cytotoxic studies were carried out by means of the MTT tassay. Methotrexate release studies from these two carriers demonstrated that the attachment of PEI-FA onto MWCNT-MTX reduces the release rate of methotrexate. The IC50 of MWCNT-MTX-PEI-FA and MWCNT-MTX have been calculated as follows: 9.89 ± 0.38 and 16.98 ± 1.07 µg/mL, respectively. Cytotoxic studies on MWCNT-MTX-PEI-FA and MWCNT-MTX in the presence of an IR laser showed that at high concentrations, they had similar toxicities due to the MWCNT's photothermal effect. Targeting effect studies in the presence of the IR laser on the cancer cells have shown that MWCNT-MTX-PEI-FA, MWCNT-MTX, and f-MWCNT have triggered the death of cancer cells by 55.11 ± 1.97%, 49.64 ± 2.44%, and 37 ± 0.70%, respectively. The release profile of MTX in MWCNT-MTX-PEI-FA showed that the presence of PEI acts as a barrier against release and reduces the MTX release rate. In the absence of a laser, MWCNT-MTX-PEI-FA exhibits the highest degree of cytotoxicity. In the presence of a laser, the cytotoxicity of MWCNT-MTX and MWCNT-MTX-PEI-FA has no significant difference. Targeting studies have shown that MWCNT-MTX-PEI-FA can be absorbed by cancer cells exclusively.

Theoretical insight into the disordered structure of (Z)-2-[(E)-(4-methoxybenzylidene)hydrazinylidene]-1,2-diphenylethanone: the role of noncovalent interactions

A global glide disorder has been discovered during an X-ray investigation of the crystal structure of (Z)-2-[(E)-(4-methoxybenzylidene)hydrazinylidene]-1,2-diphenylethanone (MHDE, C₂₂H₁₈N₂O₂) at room temperature. In another crystal, however, such disorder disappears (still at room temperature). Even though the disorder may be partly due to the poor quality of the harvested crystal, the structure can shed light on the nature of disorder. With the help of quantum chemical calculations, it is found that the global disorder seems to be connected with the need for stabilization of the somewhat rigid but mobile and unstable molecular structure. The most relevant feature driving the packing of the disordered structure concerns the slight perturbations (such as glide) of two or more disorder components (fractional occupancies) distributed throughout the crystal.

In silico study of Bombyx mori fibroin enhancement by graphene in acidic environment

Bombyx mori fibroin has been widely used since a long time ago and has become a popular material. Here, we carry out a molecular dynamics simulation-based docking simulation of a small fragment of graphene in order to seek the best binding position on the N-termini domain of Bombyx mori fibroin. We report the best binding position, of which binding free energy falls at -54.8 kJ mol-1, indicating the strong binding. The further analysis of the binding pathway shows that this position is selective for single layered graphene rather than multi-layered graphene within our limited simulation times. Via comparing the RAMAN spectra of the corresponding binding pose of atomic clusters, we report the change in the bands compared with free standing graphene fragments, implying the change in molecular orbitals.

Exploring biological effects of MoS2 nanosheets on native structures of α-helical peptides

Recent reports of mono- and few-layer molybdenum disulfide (MoS2), a representative transition metal dichacogenide (TMD), as antibacterial and anticancer agents have shed light on their potential in biomedical applications. To better facilitate these promising applications, one needs to understand the biological effects of these TMDs as well, such as their potential adverse effects on protein structure and function. Here, we sought to understand the interaction of MoS2 nanosheets with peptides using molecular dynamics simulations and a simple model polyalanine with various lengths (PAn, n = 10, 20, 30, and 40; mainly α - helices). Our results demonstrated that MoS2 monolayer has an exceptional capability to bind all peptides in a fast and strong manner. The strong attraction from the MoS2 nanosheet is more than enough to compensate the energy needed to unfold the peptide, regardless of the length, which induces drastic disruptions to the intra-peptide hydrogen bonds and subsequent secondary structures of α - helices. This universal phenomenon may point to the potential nanotoxicity of MoS2 when used in biological systems. Moreover, these results aligned well with previous findings on the potential cytotoxicity of TMD nanomaterials.

Orientational Binding of DNA Guided by the C2N Template

A detailed understanding of the interactions between biomolecules and nanomaterial surfaces is critical for the development of biomedical applications of these nanomaterials. Here, we characterized the binding patterns and dynamics of a double stranded DNA (dsDNA) segment on the recently synthesized nitrogenized graphene (C₂N) with both theoretical (including classical and quantum calculations) and experimental approaches. Our results show that the dsDNA repeatedly exhibits a strong preference in its binding mode on the C₂N substrate, displaying an upright orientation that is independent of its initial configurations. Interestingly, once bound to the C₂N monolayer, the transverse mobility of the dsDNA is highly restricted. Further energetic and structural analyses reveal that the strength and position of the binding is guided by the favorable π-π stacking between the dsDNA terminal base pairs and the benzene rings on the C₂N surface, accompanied by a simultaneous strong nanoscale dewetting that provides additional driving forces. The periodic atomic charge distributions on C₂N (from its unique porous structure) also cause the formation of local highly dense first solvation shell water clusters, which act as further steric hindrance for the dsDNA migration. Furthermore, free energy profiling calculated by the umbrella sampling technique quantitatively supports these observations. When compared to graphene, C₂N is found to show a milder attraction to dsDNA, which is confirmed by experiments. This orientational binding of DNA on the C₂N substrate might shed light on the design of template-guided nanostructures where their functions can be tuned by specialized biomolecular coating.

Graphene Oxide Nanosheets Retard Cellular Migration via Disruption of Actin Cytoskeleton

Graphene and graphene-based nanomaterials are broadly used for various biomedical applications due to their unique physiochemical properties. However, how graphene-based nanomaterials interact with biological systems has not been thoroughly studied. This study shows that graphene oxide (GO) nanosheets retard A549 lung carcinoma cell migration through nanosheet-mediated disruption of intracellular actin filaments. After GO nanosheets treatment, A549 cells display slower migration and the structure of the intracellular actin filaments is dramatically changed. It is found that GO nanosheets are capable of absorbing large amount of actin and changing the secondary structures of actin monomers. Large-scale all-atom molecular dynamics simulations further reveal the interactions between GO nanosheets and actin filaments at molecular details. GO nanosheets can insert into the interstrand gap of actin tetramer (helical repeating unit of actin filament) and cause the separation of the tetramer which eventually leads to the disruption of actin filaments. These findings offer a novel mechanism of GO nanosheet induced biophysical responses and provide more insights into their potential for biomedical applications.

Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale

Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene.

An In Silico study of TiO2 nanoparticles interaction with twenty standard amino acids in aqueous solution

Titanium dioxide (TiO₂) is probably one of the most widely used nanomaterials, and its extensive exposure may result in potentially adverse biological effects. Yet, the underlying mechanisms of interaction involving TiO₂ NPs and macromolecules, e.g., proteins, are still not well understood. Here, we perform all-atom molecular dynamics simulations to investigate the interactions between TiO₂ NPs and the twenty standard amino acids in aqueous solution exploiting a newly developed TiO₂ force field. We found that charged amino acids play a dominant role during the process of binding to the TiO₂ surface, with both basic and acidic residues overwhelmingly preferred over the non-charged counterparts. By calculating the Potential Mean Force, we showed that Arg is prone to direct binding onto the NP surface, while Lys needs to overcome a ~2 kT free energy barrier. On the other hand, acidic residues tend to form “water bridges” between their sidechains and TiO₂ surface, thus displaying an indirect binding. Moreover, the overall preferred positions and configurations of different residues are highly dependent on properties of the first and second solvation water. These molecular insights learned from this work might help with a better understanding of the interactions between biomolecules and nanomaterials.

EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution

As a major effective component in green tea, (-)-epigallocatechin-3-gallate (EGCG)'s potential benefits to human health have been widely investigated. Recent experimental evidences indicate that EGCG can induce the aggregation of HMGB1 protein, a late mediator of inflammation, which subsequently stimulates the autophagic degradation and thus provides protection from lethal endotoxemia and sepsis. In this study, we use molecular dynamics (MD) simulations to explore the underlying molecular mechanism of this aggregation of HMGB1 facilitated by EGCG. Our simulation results reveal that EGCG firmly binds to HMGB1 near Cys106, which supports previous preliminary experimental evidence. A large HMGB1 conformational change is observed, where Box A and Box B, two homogenous domains of HMGB1, are repositioned and packed together by EGCG. This new HMGB1 conformation has large molecular polarity and distinctive electrostatic potential surface. We suggest that the highly polarized charge distribution leads to the aggregation of HMGB1, which differs from the previous hypothesis that two HMGB1 monomers are linked by the dimer of EGCG. Possible aggregating modes have also been investigated with potential of mean force (PMF) calculations. Finally, we conclude that the conformation induced by EGCG is more aggregation-prone with higher binding free energies as compared to those without EGCG.

Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A4

We report a detailed computational and experimental study of the interaction of single-walled carbon nanotubes (SWCNTs) with the drug-metabolizing cytochrome P450 enzyme, CYP3A4. Dose-dependent inhibition of CYP3A4-mediated conversion of the model compound, testosterone, to its major metabolite, 6β-hydroxy testosterone was noted. Evidence for a direct interaction between SWCNTs and CYP3A4 was also provided. The inhibition of enzyme activity was alleviated when SWCNTs were pre-coated with bovine serum albumin. Furthermore, covalent functionalization of SWCNTs with polyethylene glycol (PEG) chains mitigated the inhibition of CYP3A4 enzymatic activity. Molecular dynamics simulations suggested that inhibition of the catalytic activity of CYP3A4 is mainly due to blocking of the exit channel for substrates/products through a complex binding mechanism. This work suggests that SWCNTs could interfere with metabolism of drugs and other xenobiotics and provides a molecular mechanism for this toxicity. Our study also suggests means to reduce this toxicity, eg., by surface modification.

Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities

Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.

Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructures

Underlying causes of the differential polypeptide interactions on carbon nanosurfaces of varying curvatures emerge from a synchronized computational study.

Exploration of graphene oxide as an intelligent platform for cancer vaccines

We explored an intelligent vaccine system via facile approaches using both experimental and theoretical techniques based on the two-dimensional graphene oxide (GO). Without extra addition of bio/chemical stimulators, the microsized GO imparted various immune activation tactics to improve the antigen immunogenicity. A high antigen adsorption was acquired, and the mechanism was revealed to be a combination of electrostatic, hydrophobic, and π-π stacking interactions. The "folding GO" acted as a cytokine self-producer and antigen reservoir and showed a particular autophagy, which efficiently promoted the activation of antigen presenting cells (APCs) and subsequent antigen cross-presentation. Such a "One but All" modality thus induced a high level of anti-tumor responses in a programmable way and resulted in efficient tumor regression in vivo. This work may shed light on the potential use of a new dimensional nano-platform in the development of high-performance cancer vaccines.

Destruction of amyloid fibrils by graphene through penetration and extraction of peptides

Current therapies for Alzheimer's disease (AD) can provide a moderate symptomatic reduction or delay progression at various stages of the disease, but such treatments ultimately do not arrest the advancement of AD. As such, novel approaches for AD treatment and prevention are urgently needed. We here provide both experimental and computational evidence that pristine graphene and graphene-oxide nanosheets can inhibit Aβ peptide monomer fibrillation and clear mature amyloid fibrils, thus impacting the central molecular superstructures correlated with AD pathogenesis. Our molecular dynamics simulations for the first time reveal that graphene nanosheets can penetrate and extract a large number of peptides from pre-formed amyloid fibrils; these effects seem to be related to exceptionally strong dispersion interactions between peptides and graphene that are further enhanced by strong π-π stacking between the aromatic residues of extracted Aβ peptides and the graphene surface. Atomic force microscopy images confirm these predictions by demonstrating that mature amyloid fibrils can be cut into pieces and cleared by graphene oxides. Thioflavin fluorescence assays further illustrate the detailed dynamic processes by which graphene induces inhibition of monomer aggregation and clearance of mature amyloid fibrils, respectively. Cell viability and ROS assays indicate that graphene oxide can indeed mitigate cytotoxicity of Aβ peptide amyloids. Our findings provide new insights into the underlying molecular mechanisms that define graphene-amyloid interaction and suggest that further research on nanotherapies for Alzheimer's and other protein aggregation-related diseases is warranted.

Influence of carbon nanomaterial defects on the formation of protein corona

In any physiological media, carbon nanomaterials (CNM) strongly interact with biomolecules leading to the formation of biocorona, which subsequently dictate the physiological response and the fate of CNMs. Defects in CNMs play an important role not only in material properties but also in the determination of how materials interact at the nano-bio interface. In this article, we probed the influence of defect-induced hydrophilicity on the biocorona formation using micro-Raman, photoluminescence, infrared spectroscopy, electrochemistry, and molecular dynamics simulations. Our results show that the interaction of proteins (albumin and fibrinogen) with CNMs is strongly influenced by charge-transfer between them, inducing protein unfolding which enhances conformational entropy and higher protein adsorption.

Dewetting transition assisted clearance of (NFGAILS) amyloid fibrils from cell membranes by graphene

Clearance of partially ordered oligomers and monomers deposited on cell membrane surfaces is believed to be an effective route to alleviate many potential protein conformational diseases (PCDs). With large-scale all-atom molecular dynamics simulations, here we show that graphene nanosheets can easily and quickly win a competitive adsorption of human islet amyloid polypeptides (hIAPP22-28) NFGAILS and associated fibrils against cell membrane, due to graphene's unique two-dimensional, highly hydrophobic surface with its all-sp(2) hybrid structure. A nanoscale dewetting transition was observed at the interfacial region between the fibril (originally deposited on the membrane) and the graphene nanosheet, which significantly assisted the adsorption of fibrils onto graphene from the membrane. The π-π stacking interaction between Phe23 and graphene played a crucial role, providing the driving force for the adsorption at the graphene surface. This study renders new insight towards the importance of water during the interactions between amyloid peptides, the phospholipidic membrane, and graphene, which might shed some light on future developments of graphene-based nanomedicine for preventing/curing PCDs like type II diabetes mellitus.

Surface Curvature Relation to Protein Adsorption for Carbon-based Nanomaterials

The adsorption of proteins onto carbon-based nanomaterials (CBNs) is dictated by hydrophobic and π-π interactions between aliphatic and aromatic residues and the conjugated CBN surface. Accordingly, protein adsorption is highly sensitive to topological constraints imposed by CBN surface structure; in particular, adsorption capacity is thought to increase as the incident surface curvature decreases. In this work, we couple Molecular Dynamics (MD) simulations with fluorescence spectroscopy experiments to characterize this curvature dependence in detail for the model protein bovine serum albumin (BSA). By studying BSA adsorption onto carbon nanotubes of increasing radius (featuring descending local curvatures) and a flat graphene sheet, we confirm that adsorption capacity is indeed enhanced on flatter surfaces. Naïve fluorescence experiments featuring multi-walled carbon nanotubes (MWCNTs), however, conform to an opposing trend. To reconcile these observations, we conduct additional MD simulations with MWCNTs that match those prepared in experiments; such simulations indicate that increased mass to surface area ratios in multi-walled systems explain the observed discrepancies. In reduction, our work substantiates the inverse relationship between protein adsorption capacity and surface curvature and further demonstrates the need for subtle consideration in experimental and simulation design.

The role of basic residues in the adsorption of blood proteins onto the graphene surface

With its many unique properties, graphene has shown great potential in various biomedical applications, while its biocompatibility has also attracted growing concerns. Previous studies have shown that the formation of protein-graphene corona could effectively reduce its cytotoxicity; however, the underlying molecular mechanism remains not well-understood. Herein, we use extensive molecular dynamics simulations to demonstrate that blood proteins such as bovine fibrinogen (BFG) can absorb onto the graphene surface quickly and tightly to form a corona complex. Aromatic residues contributed significantly during this adsorption process due to the strong π−π stacking interactions between their aromatic rings and the graphene sp²-carbons. Somewhat surprisingly, basic residues like arginine, also played an equally or even stronger role during this process. The strong dispersion interactions between the sidechains of these solvent-exposed basic residues and the graphene surface provide the driving force for a tight binding of these basic residues. To the best of our knowledge, this is the first study with blood proteins to show that, in addition to the aromatic residues, the basic residues also play an important role in the formation of protein-graphene corona complexes.

Interfacing proteins with graphitic nanomaterials: from spontaneous attraction to tailored assemblies

Thiscritical reviewpresents a detailed overview of the chemico-physical principles ruling the non-covalent association between proteins and fullerene, carbon nanotubes and graphene towards the creation of fascinating and innovative hybrid materials for biotechnological applications.

Noncovalent interaction of carbon nanostructures

The potential application of carbon nanomaterials in biology and medicine increases the necessity to understand the nature of their interactions with living organisms and the environment. The primary forces of interaction at the nano-bio interface are mostly noncovalent in nature. Quantifying such interactions and identifying various factors that influence such interactions is a question of outstanding fundamental interest in academia and industry. In this Account, we have summarized our recent studies in understanding the noncovalent interactions of carbon nanostructures (CNSs), which were obtained by employing first-principles calculations on various model systems representing carbon nanotubes (CNTs) and graphene. Bestowed with an extended sp(2) carbon network, which is a common feature in all of these nanostructures, they exhibit π-π interactions with aromatic molecules (benzene, naphthalene, nucleobases, amino acids), cation-π type of interactions with metal ions, anion-π interactions with anions, and other XH···π type of interactions with various small molecules (H2O, NH3, CH4, H2, etc.). CNTs are wrapped-up forms of two-dimensional graphene, and hence, it is interesting to compare the binding abilities of these two allotropes that differ in their curvature. The chirality and curvature of CNSs appear to play a major role in determining the structural, energetic, and functional properties. Flat graphene shows stronger noncovalent interactions than the curved nanotubes toward various substrates. Understanding the interactions of CNSs with organic molecules and biomolecules has gained a great deal of research interest because of their potential applications in various fields. Aromatic hydrocarbons show a strong propensity to interact with CNSs via the π-π mode of interaction rather than CH···π interaction. As DNA sequencing appears to be one of the most important potential applications of carbon nanomaterials, the study of CNS-nucleobase interactions has become quite important. The nucleobases are physisorbed on the surface of CNSs in the order G > T ≈ A > C > U, exhibiting π-π-stacking type of interaction. These interactions become stronger as the curvature of the CNSs decreases. It is also indispensable to study the interaction of nanomaterials with proteins and especially with amino acids at a molecular level to understand the drug delivery mechanism of CNSs. We have shown that the CNSs interact with small molecules by means of physisorption and thus show potential for sensor applications. The prime requisite for the exploitation of these CNSs in nanoelectronics is the tunable energy gap. We have revealed that metal ion doping modulates the HOMO-LUMO energy gap of the nanotubes significantly and thus provides a handle to tune the electronic and conductivity properties of CNTs. Moreover, metal ions tend to selectively bind with nanotubes of different chirality such as armchair and zigzag nanotubes. The reduction of planar hydrocarbon materials by lithium atoms has also been studied very systematically. We also illustrate the way in which noncovalent interactions can be used to optimize and fine-tune the properties of CNSs.

Cytotoxicity of graphene: recent advances and future perspective

Graphene, a unique two-dimensional single-atom-thin nanomaterial with exceptional structural, mechanical, and electronic properties, has spurred an enormous interest in many fields, including biomedical applications, which at the same time ignites a growing concern on its biosafety and potential cytotoxicity to human and animal cells. In this review, we present a summary of some very recent studies on this important subject with both experimental and theoretical approaches. The molecular interactions of graphene with proteins, DNAs, and cell membranes (both bacteria and mammalian cells) are discussed in detail. Severe distortions in structures and functions of these biomacromolecules by graphene are identified and characterized. For example, the graphene is shown to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules directly. More interestingly, this cytotoxicity has been shown to have implications in de novo design of nanomedicine, such as graphene-based band-aid, a potential 'green' antibiotics due to its strong physical-based (instead of chemical-based) antibacterial capability. These studies have provided a better understanding of graphene nanotoxicity at both cellular and molecular levels, and also suggested therapeutic potential by using graphene's cytotoxicity against bacteria cells.