Molecular insight into adsorption affinities of Carmustine drug on boron and nitrogen doped functionalized single-walled carbon nanotubes using density functional theory including dispersion correction calculations and molecular dynamics simulation

Abstract

We report a quantum mechanics calculation and molecular dynamics simulation study of Carmustine drug (BNU) adsorption on the surface of nitrogen (N) and boron (B) doped-functionalized single-walled carbon nanotubes. The stability of the optimized complexes is determined on the basis of relative adsorption energy (ΔE_ads). The ΔE_ads results claim that drug molecule tends to adsorb on the nitrogen and boron doped functionalized tubes with the energy values in the range of ?61.177 to ?95.806?kJ/mol. Based on the obtained results, it is observed that N-doping compared with B-doping has improved more effectively drug absorption on the surface of functionalized nanotube. The results of Atoms in Molecule calculations indicate that drug adsorbs molecularly via hydrogen bonds interactions on the surface doped-functionalized carbon nanotubes. Moreover, molecular dynamics simulation is performed to investigate the dynamics behavior of the drug molecules on the nitrogen-doped functionalized carbon nanotube (f-NNT) and functionalized carbon nanotube (f-CNT). The higher average calculated electrostatic and van der Waals energies as well as higher number of intermolecular hydrogen bonds in BNU-f-NNT in comparison with BNU-f-CNT model suggest the more effectual interaction between drug molecules and nitrogen-doped functionalized carbon nanotube.

Communicated by Ramaswamy H. Sarma     

Combination of Rolling Vibration and Serpentinite Induces the Formation of Penetration-Intermediates

Bacterial cells with nano-sized acicular materials were placed in a sliding friction field between a hydrogel and an interface-forming material, after which cells with surrounding materials, namely penetration-intermediates, were formed. This phenomenon is defined as the Yoshida effect. The Yoshida effect requires the following conditions: a nano-sized acicular material, a hydrogel, an interface-forming material, and a power source for inducing sliding friction. The penetration-intermediate in the Yoshida effect has been demonstrated to readily incorporate exogenous genes and to be transformed genetically based on the acquired genes. To predict the occurrence of the Yoshida effect in the natural environment, transformation efficiency of the penetration-intermediate with plasmid DNA was investigated, and chrysotile, gellan gum, serpentinite, and artificial rolling vibration were selected as the nano-sized acicular material, hydrogel, interface-forming material, and power source for inducing sliding friction, respectively. Colloidal solution consisting of Pseudomonas sp. or Bacillus subtilis as recipient cells, donor plasmid, and chrysotile was placed on the interface between gellan gum and the serpentinite plate. To generate a sliding friction field, the serpentinite plate in contact with gellan gum was subjected to rolling vibration at 30 to 520 Gal. The sliding friction allowed recipient bacteria to become antibiotic resistant by taking up donor plasmids. Incorporation of plasmids into bacteria at the interface of gellan gum required both rolling vibration and nano-sized acicular materials such as chrysotile. Chrysotile-bound plasmid DNA was protected from catalytic reactions by DNase I and Kpn I.     

Comparative prediction of binding affinity of Hydroxyurea anti-cancer to boron nitride and carbon nanotubes as smart targeted drug delivery vehicles

Abstract

In this study, the adsorption of Hydroxyurea (HU) onto the inner and outer surfaces of boron nitride and carbon nanotubes (CNTs) was investigated using the density functional theory calculations and molecular dynamics (MDs) simulations in aqueous solution. The values of the adsorption energy show that HU molecule is preferentially adsorbed inside of boron nitride and CNTs with the molecular axis parallel to the tubes axis, which means that the cavity of nanotubes is favorable for encapsulation of this drug. Also, it was found that the HU/boron nitride nanotube (BNNT) system is more stable than the HU/CNT system. The stability of the complexes of HU/ BNNT attributed to the formation of the intermolecular hydrogen bonds between the H atoms of HU molecule and the N atoms of BNNT, which is confirmed by Bader’s quantum theory of atoms in molecules. The natural bond orbital analysis shows the charge transfers occur from HU molecule to nanotubes in all complexes. Moreover, the adsorption of HU molecule on the surfaces of the nanotubes was investigated by explicit water models. Also, the adsorption behavior of HU on the functionalized boron nitride and CNTs is investigated to design and develop new nanocarriers for biomedical applications. Furthermore, MDs simulations are examined in the presence of one and two drug molecules. The obtained results illustrate that the lowest value of Lennard–Jones (L–J) energy between drug and nanotubes exist in the simulation system with two drug molecules.     

Predicting doxorubicin drug delivery by single-walled carbon nanotube through cell membrane in the absence and presence of nicotine molecules: a molecular dynamics simulation study

Abstract

In order to study the interaction of the anticancer agent Doxorubicin with the single-walled carbon nanotubes with different diameters as drug delivery systems, the molecular dynamics (MD) simulations have been used. Also, for design and development of intracellular Doxorubicin drug delivery systems, a series of steered MD simulations are applied to explore the possibility of encapsulated Doxorubicin–carbon nanotube penetration through a lipid bilayer in presence and absence of Nicotine molecules at different pulling rates. Our simulation results showed that in spite of the adsorption of drug molecules on the outer sidewall of the nanotubes, the spontaneous localization of one Doxorubicin molecule into the cavity of the nanovectors with larger diameters is observed. It is found that the presence of Nicotine molecules in extracellular medium increases the required force for pulling nanotube-encapsulated drug as well as the required time for penetration process, especially at higher velocity. Also, the entering process of the Nicotine molecules into the carbon nanotube causes that the encapsulated drug molecule is fully released in the hydrophobic phase of the lipid bilayer.

Communicated by Ramaswamy H. Sarma     

Self-assembly of surfactant aqueous solution confined in a Janus amphiphilic nanotube

Abstract

In recent years, Janus amphiphilic nanotubes with complex surfaces have been synthesized. However, the self-assembly behaviour of surfactant solutions confined in a Janus amphiphilic nanotube has not been investigated so far. We performed molecular simulations to investigate the morphologies and phase diagrams of a surfactant confined in Janus amphiphilic nanotube consisting of both hydrophobic and hydrophilic surfaces. We derived a phase diagram of the representative snapshots of equilibrium morphologies. Morphologies that were not observed in the bulk eventuated in confined systems. Moreover, the self-assembled structures were found to be dependent on the spatial confinement. Furthermore, the self-assembled structures confined in hydroneutral and Janus amphiphilic nanotubes were compared. The results suggested that the self-assembled structures confined in the Janus amphiphilic nanotube resembled that confined in the hydroneutral nanotube owing to a strong confinement effect. Further developments in controlling the morphologies and self-assemblies will greatly advance their applications of these materials in nanofluidic devices, or for nanopatterning.     

CD2 Promotes Human Natural Killer Cell Membrane Nanotube Formation

Membrane nanotubes are thin membranous projections that physically connect two cells. While nanotubes have been studied in human natural killer (NK) cells and are implicated in aiding NK cell cytotoxic function, requirements for their formation to susceptible target cells remain incompletely understood. Here we demonstrate that the CD2-CD58/48 receptor-ligand interaction promotes and is required for nanotube formation in human NK cells. In the CD2⁻ NK cell line YTS, a stable CD2 expression variant enabled effective nanotube formation, and was associated with better cytotoxic function. Importantly, only interactions between an NK cell and a susceptible target cell were associated with multiple nanotubes and the number of nanotubes was inversely correlated with their length. Quantitative live cell fluorescence microscopy of CD2 nanotubes revealed time-dependent enrichment and localization of CD2 to the nanotube tip, and blocking CD2 receptor-ligand interactions prevented nanotube formation. Increased nanotube formation was not simply a feature of receptor-ligand pairing, as a KIR-MHC interaction in the same cell line system failed to promote nanotube formation. Additionally, blocking LFA-1-ICAM and 2B4-CD48 receptor-ligand interactions failed to inhibit nanotube formation. Thus only specific receptor-ligand pairs promote nanotubes. CD2 also promoted nanotube formation in ex vivo NK cells suggesting that CD2 plays a crucial role in the generation of nanotubes between an NK cell and its target.     

Biomechanics of smooth adhesive pads in insects: influence of tarsal secretion on attachment performance

Many insects possess smooth adhesive pads on their legs, which adhere by thin films of a two-phasic secretion. To understand the function of such fluid-based adhesive systems, we simultaneously measured adhesion, friction and contact area in single pads of stick insects (Carausius morosus). Shear stress was largely independent of normal force and increased with velocity, seemingly consistent with the viscosity-effect of a continuous fluid film. However, measurements of the remaining force 2 min after a sliding movement show that adhesive pads can sustain considerable static friction. Repeated sliding movements and multiple consecutive pull-offs to deplete adhesive secretion showed that on a smooth surface, friction and adhesion strongly increased with decreasing amount of fluid. In contrast, pull-off forces significantly decreased on a rough substrate. Thus, the secretion does not generally increase attachment but does so only on rough substrates, where it helps to maximize contact area. When slides were repeated at one position so that secretion could accumulate, sliding shear stress decreased but static friction remained clearly present. This suggests that static friction which is biologically important to prevent sliding is based on non-Newtonian properties of the adhesive emulsion rather than on a direct contact between the cuticle and the substrate.     

Modeling the interaction between anti-cancer drug penicillamine and pristine and functionalized carbon nanotubes for medical applications: density functional theory investigation and a molecular dynamics simulation

Abstract

The present study focuses on the prediction and investigation of binding properties of penicillamine with pure (5,5) single-walled carbon nanotube (SWCNT) and functionalized SWCNT (f-SWCNT) through the B3LYP and M06-2X functionals using the 6-31G** basis set. The electronic and structural properties, adsorption energy and frontier molecular orbitals of various configurations are examined. Our theoretical results indicated that the interaction of the nanotubes with penicillamine molecule is weak so that the drug adsorption process is typically physisorption. Also, results of theoretical calculations show that the adsorption of the drug molecule on f-SWCNT is stronger with shorter intermolecular distances in comparison to pure SWCNT. The natural bond orbital (NBO) analysis of studied systems demonstrates that the charge is transferred from penicillamine molecule to the nanotubes. Furthermore, molecular dynamics (MD) simulation is employed to evaluate the dynamic and diffusion behavior of drug molecule on SWCNT and f-SWCNT. Energy results show that drug molecule spontaneously moves toward the carriers, and the van der Waals energy contributions in drug adsorption are more than electrostatic interaction. The obtained results from MD simulation confirm that the functionalization of SWCNT leads to increase in the solubility of the carrier in aqueous solution.

Communicated by Ramaswamy H. Sarma     

Stress intensity factors for a vertical surface crack in polyethylene subject to rolling and sliding contact.

Pitting wear is a dominant form of polyethylene surface damage in total knee replacements, and may originate from surface cracks that propagate under repeated tribological contact. In the present study, stress intensity factors, KI and KII, were calculated for a surface crack in a polyethylene-CoCr-bone system in the presence of rolling or sliding contact pressures. Variations in crack length and load location were studied to determine probable crack propagation mechanisms and modes. The crack tip experienced a wide range of mixed-mode conditions that varied as a function of crack length, load location, and sliding friction. Positive KI values were observed for shorter cracks in rolling contact and for all crack lengths when the sliding load moved away from the crack. KII was greatest when the load was directly adjacent to the crack (g/a = +/- 1), where coincidental Mode I stresses were predominantly compressive. Sliding friction substantially increased both KImax and KIImax. The effective Mode I stress intensity factors, Keff, were greatest at g/a = +/- 1, illustrating the significance of high shear stresses generated by loads adjacent to surface cracks. Keff trends suggest mechanisms for surface pitting by which surface cracks propagate along their original plane under repeated reciprocating rolling or sliding, and turn in the direction of sliding under unidirectional sliding contact.     

Modeling of adsorption in nanopores

Adsorption in nonporous materials has been studied using Grand Canonical Monte Carlo simulations. We discuss three types of materials: (a) a model of cylindrical pores with smooth walls, representing MCM-41 like materials, (b) a model of cylindrical pores with regular structured walls (model of carbon nanotubes) and (c) a material with crystalline wall structure (zeolites). Typical problems related to the stability of adsorbed layers have been analyzed. We have shown that the mechanism of adsorption is strongly dependent on the structure of the pore walls. In the case of amorphous walls it may lead to metastable configurations. In nanotubes, the ordered corrugation structure of walls determines the low temperature structure of the adsorbed system. In 3D ordered porous system, such as zeolites, the mechanism of adsorption is mostly determined by characteristic sites of adsorption.Figure Adsorbed atoms and energy fluctuations at the pressure of the first layer formation of krypton atoms: (a) instantaneous numbers of adsorbed atoms (per nm² of the pore wall) as a function of the time of simulation (Monte Carlo steps) observed in a relatively long run, (b) the bimodal distribution of the energy fluctuations is a consequence of the behavior of the systems as shown in (a).     

Probing the Diameter Limit of Single Walled Carbon Nanotubes in SWCNT: Fullerene Solar Cells

In this work, for the first time, the diameter limit of surfactant wrapped single walled carbon nanotubes (SWCNTs) in SWCNT:C₆₀ solar cells is determined through preparation of monochiral small and large diameter nanotube devices as well as those from polychiral mixtures. Through assignment of the different nanotube chiralities by photoluminescence and optical density measurements a diameter limit yielding 0% internal quantum efficiency (IQE) is determined. This work provides insights into the required net driving energy for SWCNT exciton dissociation onto C₆₀ and establishes a family of (n,m) species which can efficiently be utilized in polymer‐free SWCNT:C₆₀ solar cells. Using this approach the largest diameter nanotube with an IQE > 0% is found to be (8,6) with a diameter of 0.95 nm. Possible strategies to extend this diameter limit are then discussed.     

Friction and adhesion in the tarsal and metatarsal scopulae of spiders

Friction and adhesion forces of the ventral surface of tarsi and metatarsi were measured in the bird spider Aphonopelma seemanni (Theraphosidae) and the hunting spider Cupiennius salei (Ctenidae). Adhesion measurements revealed no detectable attractive forces when the ventral surfaces of the leg segments were loaded and unloaded against the flat smooth glass surface. Strong friction anisotropy was observed: friction was considerably higher during sliding in the distal direction. Such anisotropy is explained by an anisotropic arrangement of microtrichia on setae: only the setal surface facing in the distal direction of the leg is covered by the microtrichia with spatula-like tips. When the leg is pushed, the spatula-shaped tips of microtrichia contact the substrate, whereas, when the leg is pulled over a surface, setae bend in the opposite direction and contact the substrate with their spatulae-lacking sides. In an additional series of experiments, it was shown that desiccation has an effect on the friction force. Presumably, drying of the legs results in reduction of the flexibility of the setae, microtrichia, spatulae, and underlying cuticle; this diminishes the ability to establish proper contact with the substrate and thus reduces the contact forces.     

Accurate acid dissociation constant (pKa) calculation for the sulfachloropyridazine and similar molecules

In this work, the interaction of GaN nanotube (GaNNT) with common air pollutants of industrialized cities, such as NH₃, NO₂ and SO₂ in different configurations was studied. For this study, the single-walled (10,0) GaNNT was used. The analysis was done via the density functional theory implemented in the SIESTA simulation software. The analysis of the results shows that the air pollutants alter the properties of nanotubes when they interact with them. The stability analysis shows that the most stable configurations are those in which adsorption occurs through a chemical process. The systems remain semiconductors, but in the case of NO₂ and SO₂ molecules interacting with GaNNT, there was a significant reduction in the energy gap. Our results also indicate that GaNNT is a promising material to detect and remove NH₃ and NO₂ molecules from the environment; however, it may be not applicable to detect or remove SO₂, because the latter interacts strongly with the nanotube, which prevents the GaNNT from being reused.

     

Multifunctional Effect of p‐Doping,Antireflection, and Encapsulation by Polymeric Acid for High Efficiency and Stable Carbon Nanotube‐Based Silicon Solar Cells

Silicon solar cells among different types of solar energy harvesters have entered the commercial market owing to their high power conversion efficiency and stability. By replacing the electrode and the p‐type layer by a single layer of carbon nanotubes, the device can be further simplified. This greatly augments the attractiveness of silicon solar cells in the light of raw material shortages and the solar payback period, as well as lowering the fabrication costs. However, carbon nanotube‐based silicon solar cells still lack device efficiency and stability. These can be improved by chemical doping, antireflection coating, and encapsulation. In this work, the multifunctional effects of p‐doping, antireflection, and encapsulation are observed simultaneously, by applying a polymeric acid. This method increases the power conversion efficiency of single‐walled carbon nanotube‐based silicon solar cells from 9.5% to 14.4% and leads to unprecedented device stability of more than 120 d under severe conditions. In addition, the polymeric acid‐applied carbon nanotube‐based silicon solar cells show excellent chemical and mechanical robustness. The obtained stable efficiency stands the highest among the reported carbon nanotube‐based silicon solar cells.     

Simulation of carbon nanotube welding through Ar bombardment

Single-walled carbon nanotubes show promise as nanoscale transistors for nanocomputing applications. This use will require appropriate methods for creating electrical connections between distinct nanotubes, analogous to welding of metallic wires at larger length scales, but methods for performing nanoscale chemical welding are not yet sufficiently understood. This study examines the effect of Ar bombardment on the junction of two crossed single-walled carbon nanotubes, to understand the value and limitations of this method for generating connections between nanotubes. A geometric criterion was used to assess the quality of the junctions formed, with the goal of identifying the most productive conditions for experimental ion bombardment. In particular, the effects of nanotube chirality, Ar impact kinetic energy, impact particle flux and fluence, and annealing temperature were considered. The most productive bombardment conditions, leading to the most crosslinking of the tubes with the smallest loss of graphitic (i.e., conductive) character, were found to be at relatively mild impact energies (100 eV), with low flux and high-temperature (3000 K) annealing. Particularly noteworthy for experimental application, a high junction quality is maintained for a relatively broad range of fluences, from 3?×?10¹⁹ m^?2 to at least 1?×?10²⁰ m^?2.     

Morphological and Structural Studies of ZnO Nanotube Films Using Thermal Evaporation Technique

Simple thermal evaporation technique has been used to prepare Pb-doped ZnO nanotube films on Si (100) substrate. X-ray photoelectron spectroscopy (XPS) and energy-dispersive X-ray spectroscopy (EDX) characterization have been employed to investigate the element’s contents, which indicates the presence of stoichiometry ZnO nanotube film. The XRD pattern has shown the wurtzite phase of ZnO and polycrystalline structure. Thickness and morphology of the films were explored from the cross sectional of the films and the surface using scanning electron microscopy (SEM) images. SEM images have confirmed the ZnO nanotubes and modifications of the morphology when adding Pb; the recorded images have proved that the diameter of the nanotubes is about 50 nm. However, AFM and SEM images have shown dense structure (without nanotubes) for non-doped ZnO film (Pb = 0 wt.%).

     

Research on the Interstitial Fluid Load Support Characteristics and Start-Up Friction Mechanisms of PVA-HA-Silk Composite Hydrogel

Hydrogel has been extensively studied as an articular cartilage repair and replacement material. PVA-HA-Silk composite hydrogel was prepared by freezing-thawing method in this paper. Mechanical properties were determined by experiments and the friction coefficient of PVA-HA-Silk composite hydrogel against steel ball was verified using micro-tribometer. Finite Element Method （FEM） was used to study the lubrication mechanism of PVA-HA-Silk composite hydrogel and the relation between the interstitial fluid load support and the start-up friction resistance. The results show that the elastic modulus and the permeability are 2.07 MPa and 10^-15m^4N^-1s^-1, respectively, and the start-up friction coefficients of PVA-HA-Silk composite hydrogel are in the range of 0.154）.2 at different contact loads, contact time and sliding speeds. The start-up friction resistance of PVA-HA-Silk composite hydrogel increases with the contact load and contact time. With the increase in sliding speed, the start-up friction resistance of PVA-HA-Silk composite hydrogel decreases. There is an inverse relation between the start-up friction resistance and the interstitial fluid load support. The change of fluid flow with the increase in sliding displacement has an important effect on the interstitial fluid load support and friction resistance. The interstitial fluid load support decreases with the increase in contact load and contact time, while the interstitial fluid load support reinforces with the increase in sliding speed. Moreover, PVA-HA-Silk composite hydrogel has mechanical properties of recovery and self-lubricating.     

Synthetic Chloride-Selective Carbon Nanotubes Examined by Using Molecular and Stochastic Dynamics

Synthetic channels, such as nanotubes, offer the possibility of ion-selective nanoscale pores which can broadly mimic the functions of various biological ion channels, and may one day be used as antimicrobial agents, or for treatment of cystic fibrosis. We have designed a carbon nanotube that is selectively permeable to anions. The virtual nanotubes are constructed from a hexagonal array of carbon atoms (graphene) rolled up to form a tubular structure, with an effective radius of 4.53 Å and length of 34 Å. The pore ends are terminated with polar carbonyl groups. The nanotube thus formed is embedded in a lipid bilayer and a reservoir containing ionic solutions is added at each end of the pore. The conductance properties of these synthetic channels are then examined with molecular and stochastic dynamics simulations. Profiles of the potential of mean force at 0 mM reveal that a cation moving across the pore encounters an insurmountable free energy barrier of ∼25 kT in height. In contrast, for anions, there are two energy wells of ∼12 kT near each end of the tube, separated by a central free energy barrier of 4 kT. The conductance of the pore, with symmetrical 500 mM solutions in the reservoirs, is 72 pS at 100 mV. The current saturates with an increasing ionic concentration, obeying a Michaelis-Menten relationship. The pore is normally occupied by two ions, and the rate-limiting step in conduction is the time taken for the resident ion near the exit gate to move out of the energy well.