Manipulating Biomolecules with Aqueous Liquids Confined within Single-Walled Nanotubes

Unexpected spontaneous dynamic oxygen migration on carbon nanotubes

Combining density functional theory (DFT) calculations and ab initio molecular dynamics (AIMD) simulations, we show that oxygen functional groups exhibit unexpected spontaneous dynamic behaviors on the interior surface of single-walled carbon nanotubes (SWCNTs). The hydroxyl and epoxy migrations are achieved by the C-O bond breaking/reforming reactions or the proton transfer reaction between the neighboring epoxy and hydroxyl groups. It is demonstrated that the spontaneous dynamic characteristic is attributed to the sharply reduced energy barrier less than or comparable to thermal fluctuations. We also observe a stable intermediate state with a dangling C-O bond, which permits the successive migration of the oxygen functional groups. However, on the exterior surface of SWCNTs, it is difficult for the oxygen groups to migrate spontaneously because there are relatively high energy barriers, and the dangling C-O bond prefers to transform into the more stable epoxy configuration. The spontaneous oxygen migration is further confirmed by the oxygen migration process using DFT calculations and AIMD simulations at room temperature. Our work provides a new understanding of the behavior of oxygen functional groups at interfaces and gives a potential route to design new carbon-based dynamic materials.

Adjustable diffusion enhancement of water molecules in a nanoscale water bridge

The emergence of nanofluidics in the last few decades has led to the development of various applications such as water desalination, ultrafiltration, osmotic energy conversion, etc. In particular, understanding water molecule transport in nanotubes is of importance for designing novel ultrafiltration and filtering devices. In this paper, we use an electric field to form a nanoscale water bridge as an artificial water channel to connect two separate disjoint nanotubes by molecular dynamics simulations. The extended length of the water bridge under different electric field strengths could adjust the diffusion process of the water molecules crossing the two disjoint nanotubes and the diffusion coefficients could be remarkably enhanced up to 4 times larger than the value in bulk water. By analyzing the structure of the water bridge, it is found that the diffusion enhancement originates from the strengthened interactions and the increase of hydrogen bonds between the water molecules due to the restrained reorientation from the external electric field. Our result provides a promising insight for realizing an efficient mass transport between various disjoint nanochannels.

The Effect of Fibronectin Coating on Protein Corona Structure and Cellular Uptake of Single-Walled Carbon Nanotubes

Protein coating is an outstanding surface modification strategy to influence the organization of biomolecules on the interface of nanomaterials. In the present study, fibronectin (FN) was used to modify the surface chemistry of single-walled carbon nanotubes (SWNTs) and carboxylated SWNTs (CO2-SWNTs) to analyze its effects on the protein corona composition and cellular uptake. At first, the successful coating of FN on the surface of both SWNTs was confirmed by transmission electron microscopy (TEM) and Raman spectroscopy. The results showed that the biomolecular organization of SWNTs and CO2-SWNTs coronas was changed after FN coating based on the evidence obtained from the surface plasmon intensity of the samples. Moreover, the MTT assay and confocal microscopy imaging revealed less cytotoxicity and cellular uptake of SWNTs coronas in comparison to bulk samples, respectively. It is suggested that the protein coating of SWNTs can modify the corona pattern and consequently the biological behavior of carbon nanotubes.

Efficient Transport Between Disjoint Nanochannels by a Water Bridge

Water channels are important to new purification systems, osmotic power harvesting in salinity gradients, hydroelectric voltage conversion, signal transmission, drug delivery, and many other applications. To be effective, water channels must have structures more complex than a single tube. One way of building such structures is through a water bridge between two disjoint channels that are not physically connected. We report on the results of extensive molecular dynamics simulation of water transport through such bridges between two carbon nanotubes separated by a nanogap. We show that not only can pressurized water be transported across a stable bridge, but also that (i) for a range of the gap's width l_{g} the bridge's hydraulic conductance G_{b} does not depend on l_{g}, (ii) the overall shape of the bridge is not cylindrical, and (iii) the dependence of G_{b} on the angle between the axes of two nonaligned nanochannels may be used to tune the flow rate between the two.

An investigation into non-covalent functionalization of a single-walled carbon nanotube and a graphene sheet with protein G:A combined experimental and molecular dynamics study

Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with the Gra, the adsorption of the PrG on Gra did not induce significant changes in the IgG tendency. Several orientations of the PrG were adopted in the presence of SWCNT or Gra; however, SWCNT could block the PrG-FcR. Moreover, it was confirmed that SWCNT reduced the α-helical structure content in the PrG. Reduction of α-helical structure of the PrG and improper orientation of the PrG-SWCNT could remarkably decrease the PrG tendency to the Fc of the IgG. Importantly, the Gra could appropriately orient the PrG by both exposing the PrG-FcR and also by blocking the fragment of the PrG that had tendency to interact with Fab in IgG.

Reversible Hydrophobicity-Hydrophilicity Transition Modulated by Surface Curvature

Wettability (hydrophobicity and hydrophilicity) is of fundamental importance in physical, chemical, and biological behaviors, resulting in widespread interest. Herein, by modulating surface curvature, we observed a reversible hydrophobic-hydrophilic transition on a model referred to a platinum surface. The underlying mechanism is revealed to be the competition between strong water-solid attraction and interfacial water orderliness. On the basis of the competition, we further propose an equation of wetting transition in the presence of an ordered interfacial liquid. It quantitatively reveals the relation of solid wettability with interfacial water orderliness and solid surface curvature, which can be used for predicting the critical point of the wetting transition. Our findings thus provide an innovative perspective on the design of a functional device demonstrating a reversible wettability transition and even a molecular-level understanding of biological functions.

3D flexible water channel: stretchability of nanoscale water bridge

Artificial water channels can contribute to a better understanding of natural water channels and offer a highly selective, advanced conductance system. Most studies use nanotubes, however it is difficult to fabricate a flexible structure, and the nanosized diameter brings nanoconfinement effects, and nanotube toxicity arouses biosafety concerns. In this paper, we use an electric field to restrain the water molecules to form a nanoscale water bridge as an artificial water channel to connect a separated solid plate by molecular dynamics simulations. We observe strong 3D flexible stretchability in the water bridge, maintaining a variable length and an arbitrary angle for a considerably long time. The stretching of the water bridge enables it to be polarized at an arbitrary angle and the stretchability is linearly dependent upon the polarization strength. More interestingly, we show the possibility of establishing complex water networks, e.g., triangle, rectangle, hexagon, and tetrahedron-tetrahedron water networks. Our results may help realize structurally flexible and environmentally friendly water channels for lab-on-a-chip applications in nanofluidics.

Manipulation of a neutral and nonpolar nanoparticle in water using a nonuniform electric field

The manipulation of nanoparticles in water is of essential importance in chemical physics, nanotechnology, medical technology, and biotechnology applications. Generally, a particle with net charges or charge polarity can be driven by an electric field. However, many practical particles only have weak and even negligible charge and polarity, which hinders the electric field to exert a force large enough to drive these nanoparticles directly. Here, we use molecular dynamics simulations to show that a neutral and nonpolar nanoparticle in liquid water can be driven directionally by an external electric field. The directed motion benefits from a nonuniform water environment produced by a nonuniform external electric field, since lower water energies exist under a higher intensity electric field. The nanoparticle spontaneously moves toward locations with a weaker electric field intensity to minimize the energy of the whole system. Considering that the distance between adjacent regions of nonuniform field intensity can reach the micrometer scale, this finding provides a new mechanism of manipulating nanoparticles from the nanoscale to the microscale.

Porous carbon nanotubes: molecular absorption, transport, and separation

We use classical molecular dynamics simulations to study nanofluidic properties of porous carbon nanotubes. We show that saturated water vapor condenses on the porous nanotubes, can be absorbed by them and transported in their interior. When these nanotubes are charged and placed in ionic solutions, they can selectively absorb ions in their interior and transport them. Porous carbon nanotubes can also be used as selective molecular sieves, as illustrated on a room temperature separation of benzene and ethanol.

Simple and reusable picoinjector for liquid delivery via nanofluidics approach

Precise control of sample volume is one of the most important functions in lab-on-a-chip (LOC) systems, especially for chemical and biological reactions. The common approach used for liquid delivery involves the employment of capillaries and microstructures for generating a droplet which has a volume in the nanoliter or picoliter range. Here, we report a novel approach for constructing a picoinjector which is based on well-controlled electroosmotic (EO) flow to electrokinetically drive sample solutions. This picoinjector comprises an array of interconnected nanochannels for liquid delivery. Such technique for liquid delivery has the advantages of well-controlled sample volume and reusable nanofluidic chip, and it was reported for the first time. In the study of the pumping process for this picoinjector, the EO flow rate was determined by the intensity of the fluorescent probe. The influence of ion concentration in electrolyte solutions over the EO flow rate was also investigated and discussed. The application of this EO-driven picoinjector for chemical reactions was demonstrated by the reaction between Fluo-4 and calcium chloride with the reaction cycle controlled by the applied square waves of different duty cycles. The precision of our device can reach down to picoliter per second, which is much smaller than that of most existing technologies. This new approach, thus, opens further possibilities of adopting nanofluidics for well-controlled chemical reactions with particular applications in nanoparticle synthesis, bimolecular synthesis, drug delivery, and diagnostic testing.

PACS

85.85.+ j; 87.15.hj; 82.39.Wj.

Molecular switch for tuning ions across nanopores by an external electric field

Active control of ion transport in nanoscale channels is attracting increasing attention. Recently, experimental and theoretical results have verified that depending on the charged surface of nanopores, the solution inside nanopores can contain either negative or positive ions, which does not happen in macroscale channels. However, the control of the surface chemistry of synthetic nanopores is difficult and the design of nanotubes with novel recognition mechanisms that regulate the ionic selectivity of negative and positive charges remains a challenge. We present here a design for an ion-selective nanopore that is controllable by external charges. Our molecular dynamics simulations show that this remarkable selectivity can be switched from predominantly negative to positive ions and that the magnitude of the ionic flux can be varied by changing the distance of the external charges. The results suggest that the hydration structures around ions play a prominent role in the selectivity process, which is tuned by the external charge. These studies may be useful for developing ways to control the behavior, properties and chemical composition of liquids and provide possible technical applications for nanofluidic field effect transistors.

Unidirectional motion of a water nanodroplet subjected to a surface energy gradient

We perform molecular dynamics simulations to demonstrate that when a nanodroplet is confined inside a carbon nanotube (CNT), unidirectional motion can be created by a nonzero surface energy gradient. It is found that the water nanodroplet moves along the direction of increasing surface energy. The transportation efficiency of the water nanodroplet is found to be dependent on the surface energy gradient; environmental temperature; and the flexibility, diameter, and defectiveness of the CNT. It is shown that higher surface energy gradient, the smaller diameter of the CNT, and fewer defects promote higher transportation efficiency. However, when the temperature is too high or too low, the water transport across the CNT is impeded. Except for the initial stage at the relatively low environmental temperature, higher flexibility of the CNT wall reduces the transportation efficiency. It is also found that the hydrogen bonds of water molecules play a role in the dynamic acceleration process with a wavelike feature. The present work provides insight for the development of CNT devices for applications such as drug delivery, nanopumps, chemical process control, and molecular medicine.

Unravelling the Role of the Compressed Gas on Melting Point of Liquid Confined in Nanospace

Phase behaviors of the liquids in nanospaces are of particular interest to understand the thermodynamics of the liquid on the nanoscale and for their applications that involve the confined systems. However, in many cases, the inconsistent observations of melting point variation for confined liquids are often revealed by different groups. Ionic liquids are a special kind of liquid. Here, by using the merits of the nonvolatile nature of ionic liquids, we realized the encapsulation of ionic liquids inside of mesopores silica oxide nanoparticles with a complete removal of compressed gas under high-vacuum condition; the completely confined ionic liquid formed a crystalline-like phase. It was found that compressed gas plays an important role in changing the melting point of the confined ionic liquid.

Phase networks of cross-β peptide assemblies

Recent evidence suggests that simple peptides can access diverse amphiphilic phases, and that these structures underlie the robust and widely distributed assemblies implicated in nearly 40 protein misfolding diseases. Here we exploit a minimal nucleating core of the Aβ peptide of Alzheimer's disease to map its morphologically accessible phases that include stable intermolecular molten particles, fibers, twisted and helical ribbons, and nanotubes. Analyses with both fluorescence lifetime imaging microscopy (FLIM) and transmission electron microscopy provide evidence for liquid-liquid phase separations, similar to the coexisting dilute and dense protein-rich liquid phases so critical for the liquid-solid transition in protein crystallization. We show that the observed particles are critical for transitions to the more ordered cross-β peptide phases, which are prevalent in all amyloid assemblies, and identify specific conditions that arrest assembly at the phase boundaries. We have identified a size dependence of the particles in order to transition to the para-crystalline phase and a width of the cross-β assemblies that defines the transition between twisted fibers and helically coiled ribbons. These experimental results reveal an interconnected network of increasing molecularly ordered cross-β transitions, greatly extending the initial computational models for cross-β assemblies.

Molecular wire of urea in carbon nanotube: a molecular dynamics study

We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ∼20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.

Binding of blood proteins to carbon nanotubes reduces cytotoxicity

With the potential wide uses of nanoparticles such as carbon nanotubes in biomedical applications, and the growing concerns of nanotoxicity of these engineered nanoparticles, the importance of nanoparticle-protein interactions cannot be stressed enough. In this study, we use both experimental and theoretical approaches, including atomic force microscope images, fluorescence spectroscopy, CD, SDS-PAGE, and molecular dynamics simulations, to investigate the interactions of single-wall carbon nanotubes (SWCNTs) with human serum proteins, and find a competitive binding of these proteins with different adsorption capacity and packing modes. The π-π stacking interactions between SWCNTs and aromatic residues (Trp, Phe, Tyr) are found to play a critical role in determining their adsorption capacity. Additional cellular cytotoxicity assays, with human acute monocytic leukemia cell line and human umbilical vein endothelial cells, reveal that the competitive bindings of blood proteins on the SWCNT surface can greatly alter their cellular interaction pathways and result in much reduced cytotoxicity for these protein-coated SWCNTs, according to their respective adsorption capacity. These findings have shed light toward the design of safe carbon nanotube nanomaterials by comprehensive preconsideration of their interactions with human serum proteins.

DNA structural changes under different stretching methods studied by molecular dynamics simulations

We present a molecular dynamics simulation study of 22-mer DNA conformational variations obtained by stretching both 3'-termini and both 5'-termini. Stretching 3'-termini by 3.5 nm required 142 kJ mol(-1) and the force plateau was approximately 80 pN, whereas stretching 5'-termini by the same length required 190 kJ mol(-1) and the force plateau was approximately 100 pN. Stretching 3'-termini led to a larger untwisting of the double helix and the successive base pairs rolled to the side of the DNA minor groove, while stretching 5'-termini resulted in the base pairs rolling to the major groove side and reducing of the diameter of DNA molecule. The most distinctive difference between stretching 3'-termini and 5'-termini was that at the force plateau region stretching the 5'-termini resulted in breakage of the base pairs, which considerably disturbed the structure of the DNA double helix. All of the variations of base rotation and translation for both stretching methods took place when the relative length of DNA l was longer than 1.2, which was the point the force plateau appeared.

A controllable molecular sieve for Na+ and K+ ions

The selective rate of specific ion transport across nanoporous material is critical to biological and nanofluidic systems. Molecular sieves for ions can be achieved by steric and electrical effects. However, the radii of Na(+) and K(+) are quite similar; they both carry a positive charge, making them difficult to separate. Biological ionic channels contain precisely arranged arrays of amino acids that can efficiently recognize and guide the passage of K(+) or Na(+) across the cell membrane. However, the design of inorganic channels with novel recognition mechanisms that control the ionic selectivity remains a challenge. We present here a design for a controllable ion-selective nanopore (molecular sieve) based on a single-walled carbon nanotube with specially arranged carbonyl oxygen atoms modified inside the nanopore, which was inspired by the structure of potassium channels in membrane spanning proteins (e.g., KcsA). Our molecular dynamics simulations show that the remarkable selectivity is attributed to the hydration structure of Na(+) or K(+) confined in the nanochannels, which can be precisely tuned by different patterns of the carbonyl oxygen atoms. The results also suggest that a confined environment plays a dominant role in the selectivity process. These studies provide a better understanding of the mechanism of ionic selectivity in the KcsA channel and possible technical applications in nanotechnology and biotechnology, including serving as a laboratory-in-nanotube for special chemical interactions and as a high-efficiency nanodevice for purification or desalination of sea and brackish water.