CoNTub: An Algorithm for Connecting Two Arbitrary Carbon Nanotubes

Photochromic Carbon Nanomaterials: An Emerging Class of Light-Driven Hybrid Functional Materials

Photochromic molecules have remarkable potential in memory and optical devices, as well as in driving and manipulating molecular motors or actuators and many other systems using light. When photochromic molecules are introduced into carbon nanomaterials (CNMs), the resulting hybrids provide unique advantages and create new functions that can be employed in specific applications and devices. This review highlights the recent developments in diverse photochromic CNMs. Photochromic molecules and CNMs are also introduced. The fundamentals of different photochromic CNMs are discussed, including design principles and the types of interactions between CNMs and photochromic molecules via covalent interactions and non-covalent bonding such as π-π stacking, amphiphilic, electrostatic, and hydrogen bonding. Then the properties of photochromic CNMs, e.g., in photopatterning, fluorescence modulation, actuation, and photoinduced surface-relief gratings, and their applications in energy storage (solar thermal fuels, photothermal batteries, and supercapacitors), nanoelectronics (transistors, molecular junctions, photo-switchable conductance, and photoinduced electron transfer), sensors, and bioimaging are highlighted. Finally, an outlook on the challenges and opportunities in the future of photochromic CNMs is presented. This review discusses a vibrant interdisciplinary research field and is expected to stimulate further developments in nanoscience, advanced nanotechnology, intelligently responsive materials, and devices.

AROFRAG─A Systematic Approach for Fragmentation of Aromatic Molecules

We present a new systematic fragmentation scheme of polycyclic aromatic hydrocarbons (PAHs), including fullerenes and nanotubes, based on an idea to treat a sextet ring as a single unbreakable unit so that the basic unit of aromaticity remains preserved upon fragmentation. In the approach, denoted as AROFRAG (from aromatic fragmentation), a set of predefined elementary subsystems, such as naphthalene and biphenyl in the first model and larger PAHs in the second and third models, is generated with appropriate weights with the aim of reproducing the structure of the original molecule. The energies of the molecules are approximated as weighted sums of the energies of these subsystems. For symmetric cases, e.g., fullerenes, the point-group symmetry is preserved during the decomposition. The AROFRAG is used in conjunction with the molecule-in-molecule (MIM) technique to obtain an accurate description of the electronic energies. The new approach has been applied for selected graphene structures and fullerene doped with boron and nitrogen atoms, for which isomerization energies were calculated, as well as for several nanotubes and regular fullerene molecules. The combination of the third AROFRAG model and the MIM approach leads to the reproduction of electronic energies with a few milli-hartree accuracy at a fraction of the computational cost of the original method.

CONAN─Novel Tool to Create and Analyze Liquids in Confined Space

Modeling of complex liquids at solid surfaces and in confinement is gaining attention due to an increase in computer power and advancement of simulation techniques. Therefore, tools to set up structures and for analysis are needed. In this paper, we present CONAN─a Python code designed to facilitate the study of liquids interacting with solid structures, such as walls or pores. Among other things, the program provides the option to generate a variety of different structures, including carbon walls and nanotubes and their boron nitride analogs, as well as the ability to analyze various structural properties of confined and interfacial liquids. In the case of the ionic liquid 1-butyl-3-methylimidazolium acetate in carbon nanotubes of different sizes, we demonstrate the abilities of our tool. The average density within the confinement highly depends on the carbon nanotube size, and it is generally lower than the density of the bulk liquid. The arrangement of the individual species within the tube also depends on size, with radial layers forming within the tubular confinement. The density is largely increased in the respective layers, while it is drastically reduced between the layers.

Adsorption and encapsulation of melittin on covalently functionalized carbon nanotubes; a molecular dynamics simulation study

For the first time, molecular dynamics (MD) simulation was used to examine melittin's adsorption and encapsulation on covalently functionalized carbon nanotubes (fCNTs). The CNT wall and terminals were functionalized with carboxy, hydroxyl, and amine functional groups. The findings demonstrated that the melittin would be adsorbed on the fCNT's outer surface when just the CNT terminal is functionalized. On the other hand, melittin is encapsulated inside the nanotube space when the CNTs' walls and terminals are functionalized. Encapsulated melittin has an alpha-helix structure similar to melittin in a water medium. With the use of parameters like root mean square fluctuations (RMSF) and radius of gyration (Rg), the melittin conformational changes were evaluated. According to the findings, the amine functional group significantly alters the melittin's conformation. The wall and terminals fCNTs with hydroxyl and carboxyl could encapsulate melittin inside them with a stable structure. This result will be useful for the design of peptide carriers.

Miniature physical sphere-in-contact models of heterogeneous catalysts and metal nanoparticles

CONTEXT

Physical molecular models have played a fundamental role in the understanding of chemical reactions on heterogeneous catalysts and on metal nanoparticles. To date, these physical models have been based on separate models of the metal nanoparticle (NP) or surface and of the substrate and the molecular structure of reactant and product adsorbates and their intermediates. In this paper, we try to provide a new miniature physical molecular model, the sphere-in-contact model of heterogeneous catalysts and metal nanoparticles that can build inexpensive, small and efficient molecular models that can be transported or shipped easily and that depict the chemical reaction as a whole, showing reactants, intermediates, products, the metal nanoparticle bound to the substrate which can give information about a reaction mechanism. These models reveal that there are certain rules with respect to the kind of sites you observe at the metal NP interface with the support by small movement of the nanoparticle.

METHODS

We have used in this study physical molecular models using the sphere-in-contact model. This is the first time such physical models are built for heterogeneous catalytic reactions and metal nanoparticles, and they are constructed out of spheres that fuse together when exposed to water.

Development of the poly(l-histidine) grafted carbon nanotube as a possible smart drug delivery vehicle

Polyhistidine is among the cell-penetrating peptides that in an acidic environment can facilitate membrane transition. Keeping in mind that the pH of the tumor intercellular medium is ∼5.5, in this paper, we examined the functionalization of a convenient drug delivery vehicle with cell-penetrating poly(l-histidine) to provide a smart drug delivery system. Classical molecular dynamics and metadynamics simulations are used to investigate the interactions between doxorubicin, carbon nanotube, poly(l-histidine), and the cell membrane. Metadynamics simulation revealed that not only the global minimum of FES reduced in an acidic environment but also the difference between the free energy of Doxorubicin as being adsorbed on poly(l-histidine) compared to when being freely dissolved in the aqueous medium show a dramatic reduction. MD simulations showed that functionalization of carbon nanotube with poly(l-histidine) groups has no detriment effect in the adsorption of Doxorubicin. The L-J interaction between Doxorubicin and carrier at the equilibrium states reached around -600 kJ/mol, both for the pristine and functionalized carbon nanotube. The coulombic interactions for both complexes were negligible in the neutral environment. At the acidic environment, the L-J interactions retained the same values as the neutral, while the coulombic interactions showed positive values, which suggested its participation in the detachments. At the vicinity of the membrane, the complexes retain their integrity both in neutral and acidic environments. In the present work, we performed metadynamics simulation to investigate the effects of poly(l-histidine) on the adsorption capacity of the carbon nanotubes, and explore the adsorption/desorption processed of Doxorubicin on pristine and poly(l-histidine)-grafted carbon nanotube. The resulted complexes were then subjected to interact with the POPC membrane model in both acidic and neutral environments via molecular dynamic simulations. The results provided here will hopefully help in a better understanding of future drug delivery systems and be helpful in designing more efficient and smart drug delivery systems.

Torsional Fracture of Carbon Nanotube Bundles: A Reactive Molecular Dynamics Study

Carbon nanotubes individually show excellent mechanical properties, being one of the strongest known materials. However, when assembled into bundles, their strength drops dramatically. It still limit the understanding of their...

Surface functionalization of boron nitride nanosheet with folic acid: Toward an enhancement in Doxorubicin anticancer drug loading performance

Loading of the Doxorubicin (DOX) as an anticancer drug molecule on boron nitride (BN) nanosheets with different sizes, in the presence and absence of Folic Acid (FA) functional groups, are investigated using molecular dynamic simulations. The obtained results from these investigations revealed that the drug molecules are spontaneously adsorbed the carriers and form stable complexes. It is also shown that an increase the nanosheet leads to an enhancement in its capacity to adsorb the drugs. Furthermore, the conjugation of BN with the FA group not only improves the BN efficiency for the drug adsorption but also helps the drug-carrier complex to target the cancerous cells. Evaluation of interaction energies reveals that L-J interaction plays an essential role in the adsorption of the drug molecules on the BN. The radial distribution function (RDF) shows that the highest drug position probability is around 0.6 nm away from the BN surface. Atomic RDF analysis is in line with the interaction energy analysis and proved that π-π stacking contributes the most to this process. Hydrogen bond (HB) analysis also shows that, although limited, the columbic interaction can be helpful in the adsorption process. Moreover, the free energy (FE) surface is explored for a system containing a BN nanosheet, an FA group, and a DOX molecule through metadynamics simulations. The obtained results reveal that the lowest FE point located in coordinations d1 = 0.70 nm and d2 = 0.84 nm, and energetically reached -280.42 kJ/mol. It can be concluded from the FE calculations that while the FA is stuck on the substrate, DOX faces difficulty in the way it be adsorbed. In return, it will be hard for the molecule to be released from the BN surface through desorption processes in neutral pH because it faces an energy barrier with a height of ∼100 kJ/mol at 1.6 nm.

Tim4 recognizes carbon nanotubes and mediates phagocytosis leading to granuloma formation

Macrophage recognition and phagocytosis of crystals is critical for the associated fibrosis and cancer. Of note, multi-walled carbon nanotubes (MWCNTs), the highly representative products of nanotechnology, induce macrophage NLRP3 inflammasome activation and cause asbestosis-like pathogenesis. However, it remains largely unknown how macrophages efficiently recognize MWCNTs on their cell surfaces. Here, we identify by a targeted screening of phagocyte receptors the phosphatidylserine receptors T cell immunoglobulin mucin 4 (Tim4) and Tim1 as the pattern-recognition receptors for carbon crystals. Docking simulation studies reveal spatiotemporally stable interfaces between aromatic residues in the extracellular IgV domain of Tim4 and one-dimensional carbon crystals. Further, CRISPR-Cas9-mediated deletion of Tim4 and Tim1 reveals that Tim4, but not Tim1, critically contributes to the recognition of MWCNTs by peritoneal macrophages and to granuloma development in a mouse model of direct mesothelium exposure to MWCNTs. These results suggest that Tim4 recognizes MWCNTs through aromatic interactions and mediates phagocytosis leading to granulomas.

Junction-Producing Algorithm Connecting Carbon Nanotube to Carbon Nanocone to Obtain Funnel-Like Nanostructure: Nanochimney Generator

This study aims to provide a computational algorithm which contributes to the understanding and implementation of carbon nanochimneys. The structure resembles a tube ending with an inverted funnel, with a connection region that uses non-hexagonal rings as defects in order to match the boundaries of the two linked nanostructures. They are important for applications such as thermal transport, gas storage, or separation. The algorithm is written in Python 3.7 and provides a .pdb file with the coordinates of all the atoms included in the system. The parameters that can be specified are the carbon nanotube dimensions, for either armchair or zigzag conformations, five levels of disclination for the carbon nanocone along with the base diameter of the latter.

Mechanical Characterisation of Single-Walled Carbon Nanotube Heterojunctions: Numerical Simulation Study

The elastic properties of single-walled carbon nanotube heterojunctions were investigated using conventional tensile, bending and torsion tests. A three-dimensional finite element model was built in order to describe the elastic behaviour of cone heterojunctions (armchair-armchair and zigzag-zigzag). This comprehensive systematic study, to evaluate the tensile, bending and torsional rigidities of heterojunctions, enabled the formulation analytical methods for easy assessment of the elastic properties of heterojunctions using a wide range of their geometrical parameters.

Mechanical Characterization of Multiwalled Carbon Nanotubes: Numerical Simulation Study

The elastic properties of armchair and zigzag multiwalled carbon nanotubes were investigated under tensile, bending, and torsion loading conditions. A simplified finite element model of the multiwalled carbon nanotubes, without taking into account the van der Waals interactions between layers, was used to assess their tensile, bending, and torsional rigidities and, subsequently, Young's and shear moduli. Relationships between the tensile rigidity and the squares of the diameters of the outer and inner layers in multiwalled carbon nanotubes, and between the bending and torsional rigidities with the fourth powers of the diameters of the outer and inner layers, were established. These relationships result in two consistent methods, one for assessment to the Young's modulus of armchair and zigzag multiwalled carbon nanotubes, based on tensile and bending rigidities, and the other to evaluate shear modulus using tensile, bending, and torsional rigidities. This study provides a benchmark regarding the determination of the mechanical properties of nonchiral multiwalled carbon nanotubes by nanoscale continuum modeling approach.

Developing nanotube junctions with arbitrary specifications

Experimentally synthesized carbon nanotube (CNTs) junctions (either single or with 2D/3D CNT network topology) are expected to have random orientation of defect sites (non-hexagonal rings) around the junction. This random and irregular nature of the junction topology and defect characteristics is expected to affect their strength and durability as well as impact the associated mesoscopic and macroscopic properties. On the contrary, theoretical and computational studies often investigate structure-property relationships of pristine and regular junctions of carbon nanostructures. In this study, we developed a computational framework to model a variety of junction structures between CNTs with arbitrary spatial (orientation and degree of overlap) and intrinsic (chirality) specifications. The developed computational model also has the ability to tune the degree of topological defects around the junction via a variety of defect annihilation approaches. Our method makes use of the primal/dual meshing concept, where the development and manipulation of the junction nodes occur using triangular meshes (primal mesh), which is eventually converted to its dual mesh (honeycomb mesh) to render a fully covalently bonded CNT junction. Here each carbon atom has 3 bonded neighbors (mimicking sp² hybridization). Under a given set of CNT orientation, overlap and chirality specifications, the approach creates a number of CNT junction configurations with varying degrees of energetic stability, offering an opportunity to investigate the effect of topological arrangement of defects around the junction on mechanical, electrical and thermal properties. In addition, it is shown via few examples that the discussed methodology can easily be extended to create multi-junction nanotube clusters, multi-wall nanotube junctions, as well as true 3D random network structures.

An electrostatic nanosecond switch in a nanoscale water channel

We proposed a nano-scale water switch composed of CNTs. We can control the switch toggle between open and close state only by changing the direction of the external electric field.

Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations

In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and interpretations of hydrophobicity in terms of alternative but parallel signatures such as interfacial fluctuations, dewetting transitions, and enhanced fluctuation probabilities at interfaces.

Reversible diameter modulation of single-walled carbon nanotubes by acetonitrile-containing feedstock

Changing the carbon feedstock from pure ethanol to a 5 vol % mixture of acetonitrile in ethanol during the growth of vertically aligned single-walled carbon nanotubes (SWNTs) reduces the mean diameter of the emerging SWNTs from approximately 2 to 1 nm. We show this feedstock-dependent change is reversible and repeatable, as demonstrated by multilayered vertically aligned SWNT structures. The reversibility of this process and lack of necessity for catalyst modification provides insight into the role of nitrogen in reducing the SWNT diameter.

Computational algorithms for fast-building 3D carbon nanotube models with defects

Algorithms for generating defective carbon nanotubes have been developed and implemented in software. The algorithms were designed to create arrays of carbon atoms that form layers and interconnect. The parameters for construction were the following: Hamada indices that respond to topology (armchair, zigzag or chiral nanotubes) and diameter, the saturated or unsaturated nature of the nanotube, the length and, most importantly, the presence of defects that can be built individually or repetitively by rotating bonds, removing atoms, or adding additional carbon atoms. The output was written in a standard, exportable file format that contained atomic coordinates useful for further computational chemistry work.

Multiple intra-tube junctions in the inner tube of peapod-derived double walled carbon nanotubes: theoretical study and experimental evidence

The coalescence process of fullerenes in the hollow core of single walled carbon nanotubes is systematically explored by the kinetic Monte Carlo method. Two elongation (or growth) modes via the coalescence (i) between an inner tube and fullerenes and (ii) between neighboring inner tubes are identified. It is found that the coalescence of two inner tubes mostly creates a very stable intra-tube junction which is composed of multiple pentagon-heptagon pairs. As a consequence, the study predicts that the inner tube of peapod derived double walled carbon nanotubes (DWNTs) must contain many intra-tube junctions. Careful high resolution transmission electron microscopy observation on peapod-grown DWNT sample provides experimental evidence of the presence of the junctions.

Using the 19F NMR chemical shift anisotropy tensor to differentiate between the zigzag and chiral forms of fluorinated single-walled carbon nanotubes

The structural characterization of different kinds of zigzag and chiral single-walled carbon nanotubes (SWNTs) has been investigated theoretically using (19)F NMR spectroscopy. The chemical shift anisotropy (CSA) tensor is computed at different levels of theory for the (19)F nuclei in different forms of functionalized fluorinated carbon nanotubes (CNT). A set of fluorine CSA parameters comprising the span, skew, and isotropic chemical shift is computed for each form of the fluoronanotubes and multidimensional CSA parameter correlation maps are constructed. We show that these correlations are able to clearly distinguish between the chiral and zigzag forms of fluorinated carbon nanotubes (F-SWNTs). Implications for solid-state and liquid-state NMR experiments are discussed.

Atomic scale growth dynamics of nanocrystals within carbon nanotubes

The confined interior region of carbon nanotubes has proved to be an effective "nano-test-tube" to conduct chemical reactions in a restricted volume. It also benefits from being thin and relatively transparent to electrons, enabling structural characterization using high-resolution transmission electron microscopy. This permits real-time monitoring of chemical reactions with atomic resolution. Here, we have studied the dynamics of single Pr atoms released from Pr(2)@C(72) metallofullerenes. We show that the Pr atoms form small nanoclusters that subsequently coalesce to ordered, stable nanocrystals within the confines of a carbon nanotube. This process has been tracked in situ with atomic-resolution using low-voltage aberration-corrected high-resolution transmission electron microscopy. We reveal that nanocrystal formation within a nanotube does not generally occur by the addition of single atoms to one pre-existing cluster but rather through aggregation of several smaller clusters. These results provide some of the deepest insights into the dynamics of single-atom behavior in the solid state.

Reversible attachment of platinum alloy nanoparticles to nonfunctionalized carbon nanotubes

The formation of monodisperse, tunable sized, alloyed nanoparticles of Ni, Co, or Fe with Pt and pure Pt nanoparticles attached to carbon nanotubes has been investigated. Following homogeneous nucleation, nanoparticles attach directly to nonfunctionalized single-walled and multi-walled carbon nanotubes during nanoparticle synthesis as a function of ligand nature and the nanoparticle work function. These ligands not only provide a way to tune the chemical composition, size, and shape of the nanoparticles but also control a strong reversible interaction with carbon nanotubes and permit controlling the nanoparticle coverage. Raman spectroscopy reveals that the sp(2) hybridization of the carbon lattice is not modified by the attachment. In order to better understand the interaction between the directly attached nanoparticles and the nonfunctionalized carbon nanotubes, we employed first-principles calculations on model systems of small Pt clusters and both zigzag and armchair single-walled carbon nanotubes. The detailed comprehension of such systems is of major importance since they find applications in catalysis and energy storage.

Investigating the diameter-dependent stability of single-walled carbon nanotubes

We investigate the long-standing question of whether electrons accelerated at 80 kV are below the knock-on damage threshold for single-walled carbon nanotubes (SWNTs). Aberration-corrected high-resolution transmission electron microscopy is used to directly image the atomic structure of the SWNTs and provides in situ monitoring of the structural modification induced by electron beam irradiation at 80 kV. We find that SWNTs with small diameters of 1 nm are damaged by the electron beam, and defects are produced in the side walls that can lead to their destruction. SWNTs with diameters of 1.3 nm and larger are more stable against degradation, and stability increases with diameter. The effect of diameter, defects, and exterior contamination on the inherent stability of SWNTs under electron beam irradiation is investigated.

Molecular-scale quantum dots from carbon nanotube heterojunctions

Carbon nanotube heterojunctions (HJs), which seamlessly connect nanotubes of different chiral structure using a small number of atomic-scale defects, represent the ultimate scaling of electronic interfaces. Here we report the first electrical transport measurements on a HJ formed between semiconducting and metallic nanotubes of known chiralities. These measurements reveal asymmetric IV-characteristics and the presence of a quantum dot (QD) with approximately 60 meV charging energy and approximately 75 meV level spacing. A detailed atomistic and electronic model of the HJ enables the identification of specific defect arrangements that lead to the QD behavior consistent with the experiment.

Molecular dynamics study on DNA oligonucleotide translocation through carbon nanotubes

Molecular dynamics simulations are performed to study the translocation of a DNA oligonucleotide in a carbon nanotube (CNT) channel consisting of CNTs of two different diameters. A strong gravitational acceleration field is applied to the DNA molecule and water solvent as an external driving force for the translocation. It is observed that both the CNT channel size and the strength of gravitational field have significant influence on the DNA translocation process. It is found that the DNA oligonucleotide is unable to pass through the (8,8) CNT even under strong gravitational fields, which extends previous finding that DNA cannot be self-inserted into a (8,8) CNT. It is shown that the DNA can pass through the (10,10)-(12,12) and (12,12)-(14,14) CNTs with stronger gravitational field resulting in faster translocation. The translocation time tau is found to follow the inverse power law relationship with the gravitational acceleration a as tau approximately a(-1.21). The energetic analysis of the translocation process shows that there is an energy barrier for DNA translocation into the (10,10) tube from the (14,14) tube, which is in contrast to previous report that DNA can be self-inserted into a (10,10) tube from outside the CNT. This difference with previous report shows that the dynamic behavior of DNA translocation inside a CNT channel is quite different from that of DNA translocation into a CNT from outside the CNT.

CAL3JHH: a Java program to calculate the vicinal coupling constants (3 J H,H) of organic molecules

Here, we present a free web-accessible application, developed in the JAVA programming language for the calculation of vicinal coupling constant (3J(H,H)) of organic molecules with the H-Csp3-Csp3-H fragment. This JAVA applet is oriented to assist chemists in structural and conformational analyses, allowing the user to calculate the averaged 3J(H,H) values among conformers, according to its Boltzmann populations. Thus, the CAL3JHH program uses the Haasnoot-Leeuw-Altona equation, and, by reading the molecule geometry from a protein data bank (PDB) file format or from multiple pdb files, automatically detects all the coupled hydrogens, evaluating the data needed for this equation. Moreover, a "Graphical viewer" menu allows the display of the results on the 3D molecule structure, as well as the plotting of the Newman projection for the couplings.