DFT studies of COOH tip-functionalized zigzag and armchair single wall carbon nanotubes

Structure and energy calculations of pristine and COOH-modified model single wall carbon nanotubes (SWCNTs) of different length were performed at B3LYP/6-31G* level of theory. From 1 to 9 COOH groups were added at the end of the nanotube. The differences in structure and energetics of partially and fully functionalized SWCNTs at one end of the nanotube are observed. Up to nine COOH groups could be added at one end of (9,0) zigzag SWCNT in case of full functionalization. However, for (5,5) armchair SWCNT, the full functionalization was impossible due to steric crowding and rim deformation. The dependence of substituent attachment energy on the number of substituents at the carbon nanotube rim was observed.     

Carbon doped boron phosphide nanotubes: A computational study

A computational study based on density functional theory (DFT) calculations has been performed to investigate the properties of the electronic structure of carbon doped boron phosphide nanotube (C-doped BPNT). Pristine and the C-doped structures of two representative (6,0) zigzag and (4,4) armchair BPNTs have been investigated. At first, the geometries of the structures have been allowed to relax by optimization. Subsequently, NMR parameters have been calculated in the optimized structures. The results indicated that the influence of C-doping was more significant on the geometries of the zigzag model than the armchair one. The difference of band gap energies between the pristine and C-doped armchair BPNT was larger than the zigzag model. Significant differences of NMR parameters of those nuclei directly contributed to the C-doping atoms have been observed.     

Initial reactions of methyl-nitramine confined inside armchair (5,5) single-walled carbon nanotube

The dissociation and isomerization reactions of methyl-nitramine(MNA) confined inside armchair CNT(5,5) single-walled carbon nanotube were investigated by using the ONIOM (B3LYP/6-311++G**:UFF) method. The results showed that some geometries of the confined MNA were modified by the CNT(5,5) in comparison with the structure of the isolated MNA. By analyzing the relevant structures and energies involved in the dissociation and isomerization reactions, we found that the transition state structures of the isomerization reactions to form CH₃NHONO (R1) and CH₃NNOOH (R2) were modified by the confinement of CNT(5,5). However, this confinement does not evidently affect the transition state structure of the HONO elimination reaction (R3). In addition, no transition state was found for the N-N bond dissociation (R4) of the isolated MNA, but this dissociation process occurred via a transition state for the confined MNA. When MNA was confined inside CNT(5,5), the activation energies of R1, R2, and R4 were decreased obviously but the energy barrier of R3 was increased slightly. The order of activation energy for these four initial reactions was also changed by the confinement of CNT(5,5). Furthermore, it was found that the relative energies of the intermediates formed by the isomerization and dissociation of MNA were also modified by the confinement of CNT(5,5). These intermediates become more stable in the confined case than in the isolated case. It was concluded that the initial reactions of MNA could be modified evdiently by confinement within a carbon nanotube.     

On the elastic properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites using molecular dynamics simulations

Molecular dynamics simulations are used to study the physical and mechanical properties of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites. The effects of nanotube atomic structure, diameter, and volume fraction on the polymer density distribution, polymer atom distribution, stress–strain curves of nanocomposites and Young’s, and shear moduli of single-walled carbon nanotubes/poly(ethylene oxide) nanocomposites are explored. It is shown that the density of polymer, surrounding the nanotube surface, has a peak near the nanotube surface. However, increasing distance leads to dropping it to the value near the density of pure polymer. It is seen that for armchair nanotubes, the average polymer atoms distances from the single-walled carbon nanotubes are larger than the polymer atom distance from zigzag nanotubes. It further is shown that zigzag nanotubes are better candidates to reinforce poly (ethylene oxide) than their armchair counterparts.     

N$_{3}^{-}$ azide anion confined inside finite-size carbon nanotubes

In this work, the confinement of an N\(_{3}^{-}\) azide anion inside finite-size single-wall zigzag and armchair carbon nanotubes of different diameters has been studied by wave function and density functional theory. Unrelaxed and relaxed interaction energies have been computed, resulting in a favorable interaction between the guest and host system. In particular, the largest interaction has been observed for the confinement in an armchair (5,5) carbon nanotube, for which a natural population analysis as well as an investigation based on the molecular electrostatic potential has been carried out. The nature of the interaction between the two fragments appears to be mainly electrostatic, favored by the enhanced polarizability of the nanotube wall treated as a finite system and passivated by hydrogen atoms. The results obtained are promising for possible applications of this complex as a starting point for the stabilization of larger polynitrogen compounds, suitable as a high-energy density material.     

OH-functionalized open-ended armchair single-wall carbon nanotubes (SWCNT) studied by density functional theory

The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C₄₀H₂₀, C₈₀H₂₀, and C₁₄₀H₂₀) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21G level, and in some cases at the B3LYP/6-31G* level, and the energy associated with the attachment of the OH substituent was determined. The OH-group attachment energy was compared with the OH functionalization of phenanthrene and picene models and with previous results for zigzag (9.0) SWCNT systems. In comparison to zigzag SWCNTs, the armchair form is more (by about 5 to 10 kcal mol^?1) reactive toward hydroxylation.

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Figure The structures of ideal armchair (5,5) single-wall carbon nanotubes (SWCNTs) of different lengths (3.7, 8.8, and 16.0 Å for C₄₀H₂₀, C₈₀H₂₀, and C₁₄₀H₂₀) and with 1–10 hydroxyl groups at the end of the nanotube were fully optimized at the B3LYP/3-21 G level, and in some cases at the B3LYP/6-31 G* level, and the energy associated with the attachment of the OH substituent was determined.

     

Tunable differential conductance of single wall C/BN nanotube heterostructure

The transport properties and differential conductance of the heterostructures constructed by (5,5) single wall carbon nanotube (SWCNT) and (5,5) single wall boron nitride nanotube (SWBNNT) are investigated using density functional theory in combination with non-equilibrium Green’s functions. We find that the transmission conductance of (5,5) BN/C nanotube heterostructure is not only continually depressed as the BNNT region increases but also the drop of the conductance is uniform in the energy window (?1.43 eV, 1 eV), which leads to linear I–V dependence for the systems when the bias is within this energy range. Moreover, the differential conductance linearly decreases when n?≤?3 but exponentially decreases when n?≥?3 for (5,5)(BN) _n /C heterostructure. Such tunable differential conductance of (5,5) BN/C nanotube heterostructure mainly derives from the blockage of the transport channels induced by the semiconductive BN segment.

The influence of the carbon nanotube on the structural and dynamical properties of cholesterol cluster

We have performed the molecular dynamics simulations for the free cholesterol cluster and the same cluster located near the carbon nanotube. We have found that the cholesterol molecules quite evenly cover the surface of single walled armchair (10, 10) carbon nanotube, forming the molecular layer. Moreover, the characteristic alignment of cholesterol molecules within the layer (along the nanotube) is observed. The comparison of the structural and dynamical observable characterizing cholesterol molecule is presented and discussed, both for the cluster with and without the presence of the nanotube.     

Molecular modeling of dissociative and non-dissociative chemisorption of nitrosamine on close-ended and open-ended pristine and Stone-Wales defective (5,5) armchair single-walled carbon nanotubes

The nitrosamine adsorbed on close-ended and open-ended pristine and Stone-Wales defective (5,5) armchair single-walled carbon nanotubes (SWCNTs) was studied using the B3LYP/6-31G(d) method. Structure optimization of all possible adsorption configurations based on the combination of two nitrosamine (amino- and imino-) isomers and four types of nanotubes was carried out. The most stable configuration for the nitrosamine adsorbed on the (5,5) armchair SWCNTs was found to be dissociative chemisorption. The adsorption energies of the most stable structures of the adsorption complexes of close-ended and open-ended pristine SWCNTs with the imino isomer of nitrosamine were −127.15 and −137.14 kcal mol⁻¹, respectively.     

Computational study of Au_4 cluster on a carbon nanotube with and without defects using QM/MM methodology

We use ONIOM (QM/MM) methodology to carry out geometry calculations in a 4-atom nanocluster supported by an (8, 8) armchair carbon nanotube with and without defects employing LSDA/SDD for the QM system and UFF for MM. In two particular cases, defects were added in the carbon nanotube wall. These defects are a double oxygenated vacancy (Vac(2)O(2)) and a double vacancy but without oxygen which creates two pentagons and an octagon. Our results show how geometries using QM/MM and energies calculations carried out with QM, change on both the gold nanocluster and the carbon nanotube. In addition, an application of ONIOM methodology in a comparative study to predict behavior of structures as hybrid materials based in carbon nanotubes combined with gold nanoclusters is shown. In this work we examine geometry changes on both the gold nanocluster and the carbon nanotube. A comparison is made with the binding energy resulting values as well as with the orbital energies such as the frontier orbitals HOMO and LUMO.     

A novel high resolution micro-radiotherapy system for small animal irradiation for cancer research

Micro-radiotherapy (micro-RT) system is specially designed for small animal (cancer cell) irradiation for basic and translational cancer research. We use carbon nanotube (CNT) field emission technology to develop a novel micro-RT system for image-guided high precision irradiation that is similar to the state of the art radiotherapy which our cancer patients receive today at mouse scale. Through the field emission control of its individually addressable x-ray pixel beams the micro-RT system electronically shapes the radiation field and forms intensity modulation pattern. In this paper, we present the development of a carbon nanotube field emission cathode array chip--a key component for our novel micro-RT system. The prototype micro-RT CNT field emission cathode array chip has 5 x 5 individually addressable cathode pixels that are 1 mm in diameter and 2 mm in pitch. An individual CNT cathode pixel is predicted to generate a dose rate in the order of 100 cGy/min at the center of the irradiated mouse based on our Monte Carlo simulation. The temporal and spatial resolutions of the micro-RT system are expected to be approximately ms level and < 2 mm respectively.     

Translational dynamic friction analysis of double-walled carbon nanotubes

Conflicting results on the effects of commensurability, overlap area, helicity and end configuration of double-walled carbon nanotubes (DWCNTs) on translational intertube friction have been reported. We perform molecular dynamics simulations on DWCNTs with different commensurabilities, overlap areas, helicities and end configurations to analyse the intertube friction behaviour and clarify these results. It is found that commensurability and overlap area play an insignificant role, while the atomic configurations of nanotube ends play a dominant role: armchair, normal and reconstructed zigzag ends contribute little to intertube friction; while the irregular ends with dangling atoms greatly increase the friction force. This end effect may also explain the role of helicity in the intertube friction. Implications of the end effect on experimental observations are also discussed.     

Gigahertz frequency tuner based on a telescoping double-walled carbon nanotube: molecular dynamics simulations

The schematics of a gigahertz-range tuner is addressed as an application of a telescoping multi-walled carbon nanotube (CNT) that can be used repeatedly, and its dynamic operation is investigated via classical molecular dynamics simulations based on a (5,5)(10,10) double-walled CNT. Fine control of the telescoped length of the double-walled CNT enables its resonance frequency to be matched to one of the signal frequencies, and the telescoped nanotube can be tuned to its resonance frequency for use as a component of a bandpass filter.     

Correlation between mRNA structure of the coding region and translational pauses.

Discontinuous translational elongation of polypeptides is observed during spider dragline silk fibroin synthesis (1,2). The repeating segment of one of the two subunit proteins constituting spider major ampullate (dragline) silk of Nephila clavipes, Spidroin 2, consists of alternate alanine-rich and proline-rich regions (3). It was found that the calculated free energy of the secondary structure of Spidroin 2 mRNA per nucleotide for the alanine-rich region is about the same as that for the successive proline-rich region. The small stability changes of local mRNA secondary structures along the mRNA chain suggest that the translational pauses observed for dragline silk fibroin synthesis may not be correlated with Spidroin 2 mRNA structure, in contrast to Spidroin 1 mRNA structure which may explain the translational pauses (4).     

First-principles simulations of the chemical functionalization of (5,5) boron nitride nanotubes

We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-Handy within the generalized gradient approximation (HCTH-GGA). We use the base function with double polarization DNP. To determine the (5,5) BNNT-SH and (5,5) BNNT-OH relaxed structures the minimum energy criterion is applied considering six different geometries depending upon the SH and OH functional groups orientation: (C1) The adsorbed functional group is oriented toward the N atom, (C2) the functional group is oriented toward the B atom, (C3) the functional group is at the central hexagon of the BNNT surface. The (C4) fourth and (C5) fifth configurations are formed by allowing bonds (of S or O) with B or N atoms at one end of the nanotube. (C6) The sixth geometry is obtained by placing the functional group at the center of one end of the BNNT. The (5,5) BNNT-SH system, in vacuum, suffers a semiconductor to metal transition while the (5,5) BNNT-OH system retains the semiconductor behavior. When structures are solvated in water these systems behave as semiconductors. The polarity increases as a consequence of the functional group-nanotube interactions no matter if they are in vacuum or in solvation situation, which indicates the possible solubility and dispersion. According to the work function the best option to construct a device is with the BNNT-OH system.     

Tuning hydrogen storage of carbon nanotubes by mechanical bending: theoretical study

The effects of mechanical bending on tuning the hydrogen storage of titanium functionalised (4,0) carbon nanotube have been assessed using density functional theory calculations with reference to the ultimate targets of the US Department of Energy (DOE). The assessment has been carried out in terms of physisorption, gravimetric capacity, projected densities of states, statistical thermodynamic stability and reaction kinetics. The Ti atom binds at the hollow site of the hexagonal ring. The average adsorption energies (?0.54 eV) per hydrogen molecule meet the DOE target for physisorption (?0.20 to ?0.60 eV). The curvature attributed to the bending angle has no effect on the average adsorption energies per H₂ molecule. With no metal clustering, the system gravimetric capacities are expected to be as large as 9.0 wt%. The reactions of the deformed (bent) carbon nanotube have higher probabilities of occurring than those of the un-deformed carbon nanotube. The Gibbs free energies, enthalpies and entropies meet the ultimate targets of the DOE for all temperatures and pressures. The closest reactions to zero free energy occur at (378.15 K/2.961 atm.) and reverse at (340 and 360 K/1 atm.). The translational component is found to exact a dominant effect on the total entropy change with temperature. Favourable kinetics of the reactions at the temperatures targeted by DOE are reported regardless of the applied pressure. The more preferable thermodynamic properties assigned to the bending nanotube imply that hydrogen storage can be improved compared to the nonbending nanotube.     

Studies on (Na+ + K+)-activated ATPase. XLII. Evidence for two classes of essential sulfhydryl groups.

1. Preincubation of purified (Na+ + K+)-ATPase (ATP phosphohydrolase, EC 3.6.1.3) preparations from rabbit kidney outer medulla with 5,5'-dithiobis-(2-nitrobenzoic acid) inhibits the (Na+ + 5+)-ATPase and K+-stimulated 4-nitro-phenylphosphatase activities. Phosphorylation of the enzyme by ATP and the Na+-stimulated ATPase activity are inhibited to the same extent as the (Na+ + K+)-ATPase activity, whereas the K+-stimulated 4-nitrophenylphosphatase activity is inhibited much less. 2. Titration with 5,5'-dithiobis-(2-nitrobenzoic acid) in sodium dodecyl sulphate shows the presence of 36 reactive sulfhydryl groups per molecule (Na+ + K+)-ATPase (Mr = 250 000). 3. Treatment with N-ethylmaleimide, resulting in complete inhibition of (Na+ + K+)-ATPase activity, leads to modification of 26 sulfhydryl groups, whereas treatment with 5,5'-dithiobis-(2-nitrobenzoic acid) results in modification of 12 sulfhydryl groups under the same conditions. 4. The reaction of N-ethylmaleimide with an essential SH-group is not prevented by previous blocking of sulfhydryl groups with 5,5'-dithiobis-(2-nitrobenzoic acid). 5. These findings indicate the existence of at least two classes of sulfhydryl groups on the enzyme, each containing at least one vital group. The difference between these classes consists in their different reactivity towards 5,5'-dithiobis-(2-nitrobenzoic acid) and N-ethylmaleimide.     

Influence of odd and even number of Stone–Wales defects on the fracture behaviour of an armchair single-walled carbon nanotube under axial and torsional strain

Using Brenner's bond-order potential to represent the interaction of the in-plane C–C bond, an armchair (8,8) single-walled carbon nanotube is investigated by molecular dynamics simulation under axial loading and twist, both for perfect and imperfect lattices introducing an increasing number of Stone–Wales (SW) defects. The Young modulus, shear modulus, tensile strength, shear strength, ductility, stiffness and toughness are computed. All the mechanical characteristics are found to change appreciably by the inclusion of SW defects. Two distinct patterns of fracture mode are observed with odd and even numbers of defects. A clear evidence of the defect–defect interaction is observed when more than one defect is included.     

Dissociation of mRNA cytoplasmic polyadenylation from translational activation by structural modification of the 5'-UTR.

During early metazoan development, certain maternal mRNAs are translationally activated by elongation of their poly(A) tails. Bicoid ( bcd ) mRNA is a Drosophila maternal mRNA that is translationally activated by cytoplasmic polyadenylation during the first hour after egg deposition. The sequences necessary and sufficient to promote its poly(A) elongation, and hence translation, are contained within its 3'-untranslated region (UTR). The mechanism by which poly(A) elongation at the 3'-end affects translational initiation at the 5'-end remains unknown. To investigate this question, we have analyzed a bicoid mRNA whose 5'-UTR contains a short antisense sequence directed against a portion of the coding region. This mutated RNA is efficiently translated in vitro. After injection into Drosophila embryos, this RNA is stable and polyadenylated, but inefficiently translated. These experiments show that structural modification of the 5'-end of an mRNA can perturb the translational activation normally conferred by polyadenylation in vivo.