Confinement of molecules and atoms inside nano-containers (NaCons) provides a powerful strategy for creating original hybrid nanostructures and studying structures and chemical properties of individual molecules at the nanoscale. Carbon nanotubes (CNTs) used as NaCons offer different advantages: (1) CNTs are built of sp2carbon atoms held together by strong covalent bonds; (2) They are thermally stable (around 700 °C in air and up to 2800 °C in vacuum); (3) mechanically more robust (with tensile strength much higher than that of steel) than any other molecular or supramolecular NaCons; (4) Their hollow core has very low chemical reactivity. The nanotube diameter is the most important parameter in determining whether or not a molecule can be trapped inside a CNT. Once encapsulated, the behavior of the guest molecule is greatly affected by confinement.We consider here Single-walled carbon nanotubes (SWNTs) having a one-dimensional hollow space of 0.4-2.0 nm that can encapsulate various molecules leading to hybrid nanotubes. Two examples will be reported, the first one concerning the encapsulation of Poly-iodides inside SWNTs; the second one related to the encapsulation of conducting oligomers into SWNTs.We will firstly show that 1D-confinement of polyiodides (In) inside SWNTs lead to specific structural arrangement of iodine species as a function of the SWCNT diameters [1]. Evidence for long range one dimensional ordering of the iodine species is shown by X-ray and electron diffraction experiments independently of the tube diameter. Using X-ray absorption spectroscopy, we show that the confinement influences the local arrangement of the chains. Below a critical diameter c of 1 nm, long linear In are evidenced leading to a weaker charge transfer than for nanotube diameter above c. A shortening of the In is exhibited with the increase of the nanotube diameter leading to a more efficient charge transfer. This point reflects the 1D-confinement of the polyiodides inside the nanotubes.Concerning the study on the confinement of conducting oligomers into SWNTs [2], we evidence by means of Raman spectroscopy and transmission electron microscopy that the supramolecular organizations of the confined oligothiophenes depend on the nanocontainer size. The Raman radial breathing mode frequency is shown to be monitored by both the number of confined molecules into a nanotube section and the competition between oligothiophene/oligothiophene and oligothiophene/tube wall interactions.

Due to their hollow space, nanotubes NT can host molecules giving rise to new hybrid molecule@NT systems. A possible class of molecules that can be hosted by nanotubes are π-conjugated oligomers which are attractive due to their electronic and optoelectronic properties[3]. Its drawback are brittleness and low electric conductivity[4]. Encapsulation of dimethyl-quaterthiophene (4TCH3) inside SWCNTs gives rise to a hybrid material, expected to combine the protection of the confining matrix to the photo-physical properties of the encapsulated unit. This hybrid material will be referred hereafter as 4TCH3@NTφ(where φ is the nanotube diameter in Å).The first recent experimental study, based on Raman spectroscopy, brought the proof that the number of encapsulated molecules depend on the size of the confining matrix[5]. Some influence of the diameter of the nanotube on the confinement state of the molecule as well as their interaction with the nanotube is expected. Inelastic neutron scattering, mostly sensitive to the confined molecule, due to the strong cross-section of hydrogen atoms, probes wide Q vector range, which is a very interesting tool in order to obtain a complete picture of the vibrational properties of such system.We are interested on the confinement properties of two hybrid systems: 4TCH3@NT09 and 4TCH3@NT14. Those materials were studied by means of inelastic neutron scattering (INS) at two instruments at the Institute Laue-Langevin, time-of-flight IN4C and Triple Axis IN1-Lagrange spectrometers. The resulting experimental HPDOS can be compared to the DFT-simulated HPDOS, allowing thus the assignment of main vibrational modes. We show that specific vibrational modes undergo to modifications upon a change of the size of the confining matrix, evidencing the influence of encapsulation in such molecules.

Many canonical processes in molecular biology rely on the dynamic assembly of higher-order nucleoprotein complexes. In bacteria, the assembly mechanism of ParABS, the nucleoprotein super-complex that actively segregates the bacterial chromosome and many plasmids, remains elusive. We combined super-resolution microscopy, quantitative genome-wide surveys, biochemistry, and mathematical modeling to investigate the assembly of ParB at the centromere-like sequences parS. We found that nearly all ParB molecules are actively confined around parS by a network of synergistic protein-protein and protein-DNA interactions. Interrogation of the empirically determined, high-resolution ParB genomic distribution with modeling suggests that instead of binding only to specific sequences and subsequently spreading, ParB binds stochastically around parS over long distances. We propose a new model for the formation of the ParABS partition complex based on nucleation and caging: ParB forms a dynamic lattice with the DNA around parS. This assembly model and approach to characterizing large-scale, dynamic interactions between macromolecules may be generalizable to many unrelated machineries that self-assemble in superstructures.