Imaging of conformational changes of biotinylated triamide molecules covalently bonded to a carbon nanotube surface

A diamide molecule bearing a biotin terminus was bonded via an amide linkage to the surface of an aminated single-walled carbon nanotube and examined by a high-resolution transmission electron microscope. The still and movie images allowed us to study not only the conformation of the molecule but also its time evolution. An iterative sequence of modeling and simulation allowed us to assign one plausible conformation out of >10(8) possibilities. The images also provide direct support for the accepted wisdom that the curved regions of pristine carbon nanotubes are chemically reactive.     

Aligned double-walled carbon nanotube long ropes with a narrow diameter distribution

Aligned double-walled carbon nanotube (DWNT) long ropes with a narrow diameter distribution were directly synthesized by sulfur-assisted floating catalytic decomposition of methane. The DWNT ropes are typically up to several centimeters in length and possess good alignment and high purity. High-resolution transmission electron microscopy (HRTEM) images and resonant Raman spectra revealed that the outer and inner tube diameters of the DWNTs are narrowly distributed in the range of 1.7-2.0 and 1.0-1.3 nm, respectively. Moreover, based on the resonant Raman measurements, the electronic properties of the two constituent tubes of the DWNTs were identified. The successful synthesis of such DWNTs opens the possibility for their fundamental studies and further applications as nanomechanical, nanooptical, and nanoelectronic devices.     

Cobalt-filled apoferritin for suspended single-walled carbon nanotube growth with narrow diameter distribution

Cobalt-filled apoferritin (Co-ferritin) was, for the first time, used as a wet catalyst for the synthesis of single-walled carbon nanotubes (SWNTs) with narrow diameter distribution. Co-ferritins were spin-coated and converted to cobalt nanoparticles by calcination. Using chemical vapor deposition, suspended networks of SWNTs were formed on pillar-structured substrates. The suspended SWNTs show narrow tube diameter distribution with a relatively good graphite structure. By virtue of the low diffusion coefficient of cobalt, Co-ferritin might be more useful for narrow diameter SWNTs growth than ferritins, which encase iron particles.     

Molecular rectification through electric field induced conformational changes

A new approach for the design of a molecular rectifier is proposed. Using a simple model, we have shown that conformational changes induced by the electric field may lead to a rectifying junction. The simplest possible rectifier of this kind presents two almost isoenergetic conformations, with different conductances and dipole moments. A simple equation allows for the estimation of the range of molecular parameters and temperatures that lead to an effective rectification. Examples show that rectification based on this mechanism is also possible at room temperature.     

Confinement of Mg-MgH2 systems into carbon nanotubes changes hydrogen sorption energetics

The density functional theory (DFT) method was used to study the effect of nanoconfinement on the energetics of Mg-MgH2 systems. Varying levels of loading of the Mg/MgH2 particles into a (10,10) carbon nanotube were examined, and the corresponding energetics were computed. A clear trend was observed that, as the level of loading increases (increasing confinement), the net energy change in the hydrogen sorption/desorption processes decreases to a significant level when the loading approaches the maximum. The confinement was found not to depend on the tube length of the confining nanotubes.     

Electric-field induced elastic stretching of multiwalled carbon nanotube clusters: a realistic model

The oscillating electric-field induced stretching phenomenon of multiwalled carbon nanotube (MWCNT) clusters in liquid crystal medium demonstrates distinct threshold behaviour under optical microscopic investigation. The optimum field required for the initiation of MWCNT cluster stretching is found to depend on their length in the field-off state. The phenomenon has been explained in light of a classical theoretical model assuming MWCNT agglomerates as a single electric dipole. The spring constant and induced charge obtained by fitting the formulated theoretical model show good agreement with previous reports, hence establish the proposed dipolar reorientation mechanism of MWCNT clusters induced by the electric field.     

Thermally induced conformational changes in poly(vinyl chloride)

Fourier transform infrared spectroscopy has been used for the detection of thermally induced conformational changes in atactic poly(vinyl chloride) (PVC). Difference spectra emphasize changes in the distribution of gauche defects in the chains as functions of temperature and annealing. Specific bands in the ν(CCl) and δ(CH₂) regions varied with inverse temperature, allowing a calculation of the activation energies of the rotamer species. Conformational changes were also detected in quenched PVC films as a result of annealing below the glass transition temperature, T_g.     

Lattice dynamics of carbon chain inside a carbon nanotube

Based on the density functional theory, we obtain the optimum geometry of carbon chain inside a carbon nanotube. The phonon spectrum and specific heat of such a chain and nanotube hybrid system are calculated in terms of lattice dynamics theory. Some new phonon branches that have been obtained come from the coupling vibrations of the nanotube and the chain. The bending and stretching modes of the chain appear at about 520 cm(-1)and 1935 cm(-1) at Gamma point, respectively. It is found that the softening of G modes results mainly from the chain induced variations in the bond length on nanotube, independent of van der Waals interaction, while the stiffening of radial breathing mode is developed by the competition between the two factors. In the low-frequency region, the vibrational density of states are very different from that of the bare nanotube. Its specific heat implies the underlying quantized phonon structures and much large thermal conductivity in the hybrid system. In addition, the chain-length dependent vibration modes are calculated, from which it is expected that a finite chain of about 14 carbon atoms in the nanotube may produce the experimental Raman peak at about 1850 cm(-1).     

Nonadiabatic effects on peptide vibrational dynamics induced by conformational changes

Quantum dynamical simulations of vibrational spectroscopy have been carried out for glycine dipeptide (CH(3)-CO-NH-CH(2)-CO-NH-CH(3)). Conformational structure and dynamics are modeled in terms of the two Ramachandran dihedral angles of the molecular backbone. Potential energy surfaces and harmonic frequencies are obtained from electronic structure calculations at the density functional theory (DFT) [B3LYP/6-31+G(d)] level. The ordering of the energetically most stable isomers (C(7) and C(5)) is reversed upon inclusion of the quantum mechanical zero point vibrational energy. Vibrational spectra of various isomers show distinct differences, mainly in the region of the amide modes, thereby relating conformational structures and vibrational spectra. Conformational dynamics is modeled by propagation of quantum mechanical wave packets. Assuming a directed energy transfer to the torsional degrees of freedom, transitions between the C(7) and C(5) minimum energy structures occur on a sub-picosecond time scale (700...800 fs). Vibrationally nonadiabatic effects are investigated for the case of the coupled, fundamentally excited amide I states. Using a two state-two mode model, the resulting wave packet dynamics is found to be strongly nonadiabatic due to the presence of a seam of the two potential energy surfaces. Initially prepared adiabatic vibrational states decay upon conformational change on a time scale of 200...500 fs with population transfer of more than 50% between the coupled amide I states. Also the vibrational energy transport between localized (excitonic) amide I vibrational states is strongly influenced by torsional dynamics of the molecular backbone where both enhanced and reduced decay rates are found. All these observations should allow the detection of conformational changes by means of time-dependent vibrational spectroscopy.     

Surface stress changes induced by the conformational change of proteins

A potential binding assay based on conformational-change-induced micromechanical motion is described. Calmodulin was used to modify a microcantilever (MCL) by a self-assembled layer-by-layer approach. The results showed that the modified MCL bent when the proteins changed their conformation upon binding with Ca2+. The cantilever deflection amplitudes were different under different ionic strengths, indicating different degrees of conformational change of the proteins in these conditions. On the contrary, cantilevers modified by proteins, such as hemoglobin and myoglobin, that do not change conformations upon binding with analytes do not cause the cantilever deflection. These results suggest that the conformational changes of proteins may be used to develop cantilever biosensors, and the MCL system has potential for use in label-free, protein-analyte screening applications.     

Protein stability at a carbon nanotube interface

The interactions of proteins with solid surfaces occur in a variety of situations. Motivated by the many nanoengineering applications of protein-carbon nanotube hybrids, we investigate the conformational transitions of hen egg white lysozyme adsorbed on a carbon nanotube. Using a C(α) structure-based model and replica exchange molecular dynamics, we show how the folding/unfolding equilibrium of the adsorbed protein varies with the strength of its coupling to the surface. The stability of the native state depends on the balance between the favorable entropy and unfavorable enthalpy change on adsorption. In the case of a weakly attractive surface when the former dominates, the protein is stabilized. In this regime, the protein can fold and unfold while maintaining the same binding fraction. With increasing surface attraction, the unfavorable enthalpic effect dominates, the native state is destabilized, and the protein has to extensively unbind before changing states from unfolded to folded. At the highest surface coupling, the entropic penalty of folding vanishes, and a folding intermediate is strongly stabilized. In this intermediate state, the α-domain of lysozyme is disrupted, while the β-sheet remains fully structured. We rationalize the relative stability of the two domains on the basis of the residue contact order.     

Confinement crystallization of poly(l-lactide) induced by multiwalled carbon nanotubes and graphene nanosheets

Journal of Thermal Analysis and Calorimetry - Two sets of multiwalled carbon nanotubes (MWCNTs)/PLLA nanocomposites and graphene nanosheets (GNSs)/PLLA nanocomposites with various MWCNTs and GNSs...     

Orientation of a benzene molecule inside a carbon nanotube

Benzene molecules confined in carbon nanotubes of varying radii are employed as semiconductors in electronic nanodevices, and their orientation determines the electrical properties of the system. In this paper, we investigate the interaction energy of all the possible configurations of a benzene molecule inside various carbon nanotubes and then we determine the equilibrium configuration. We adopt the continuous approach together with the semi-empirical Lennard-Jones potential function to model van der Waals interaction between a benzene molecule and a carbon nanotube. This approach results in an analytical expression, which accurately approximates the interaction energy and can be readily used to generate numerical data. We find that horizontal, tilted and perpendicular configurations on the axis of the carbon nanotube are all possible equilibrium configurations of the benzene molecule when the radius of the carbon nanotube is less than 5.580 Å. However, when the radius of the carbon nanotube is larger than 5.580 Å an offset horizontal orientation is the only possible equilibrium configuration of the benzene molecule. In the limiting case, the orientation of a benzene molecule on a graphene sheet can be derived simply by letting the radius of the carbon nanotube tend to infinity.     

Noncovalent attachment of pyro-pheophorbide a to a carbon nanotube

Pyrene mediated noncovalent attachment of a chlorophyll derivative, pyro-pheophorbide a, to a soluble single wall carbon nanotube is reported and the resultant CD, UV-Vis absorbance, fluorescence and 1H NMR spectra are discussed.     

Structural recovery mechanism after shear induced orientation of multiwalled carbon nanotube in polypropylene matrix

In this work the flow induced orientation and the governing mechanism of structural recovery of multi-walled carbon nanotube (MWCNT) filled polypropylene nanocomposites were investigated. A series of linear and nonlinear melt rheological measurements including stress growth and time sweep experiments were performed at different temperatures to study the structural breakdown, nanoparticles orientation, subsequent structural recovery and MWCNT loadings. The results showed that the structural recovery occurred in two stages. The first stage, initial agglomeration, showed a quick recovery which was independent of temperature, can be interpreted in terms of inter-particle van der Waals interactions. This structural recovery stage had major contribution in the storage modulus increment. The second stage of the recovery, secondary agglomeration, was slower and dependent on temperature, can be attributed to rotary diffusion of nanoparticles. This stage had minor contribution to the storage modulus increase. Storage modulus increment in both of these agglomeration was attributed to the increase of nanotube-nanotube contacts. Both of these stages were confirmed by transmission electron micrographs. These result were in a good agreement with those calculated using van der Waals and diffusion concepts.