Solid-state fingerprints of molecular threading detected by inelastic neutron scattering

Adsorption of Fumaramide [2]Rotaxane and Its Components on a Solid Substrate: A Coverage-Dependent Study

The coverage-dependent adsorption on Au(111) of a fumaramide [2]rotaxane and its components, a benzylic amide macrocycle and a fumaramide thread, is studied using high-resolution electron energy loss spectroscopy (HREELS). Up to monolayer coverage, the relative intensity of out-of-plane to in-plane phenyl ring vibrational modes indicates that the macrocycle adopts an orientation with the phenyl rings largely parallel to the surface. The formation of a chemisorption bond is evidenced by the presence of a Au-O stretching vibration. In contrast, the thread shows no evidence of chemisorption or a preferential orientation. The introduction of the thread into the macrocycle partly disrupts the film order so that the resulting chemisorbed rotaxane shows intermediate behavior with a preferential orientation up to 0.5 ML coverage. A decrease in film order and the absence of a preferred molecular orientation is observed for all three molecules at multilayer coverages. The spectral differences are addressed by molecular dynamics simulations in terms of the mobility of the phenyls of the three molecules on Au(111).

Guest Dynamics in Endohedrally Doped Fullerenes

We use molecular dynamics to calculate the vibrational density of states of several endohedral mono-metallofullerenes and compare the results with the experimental values. The vibrational patterns depend weakly on the charge transfer from the metal to the fullerene cage, with the largest variations of approximately 2 cm(-1) observed upon switching off completely the Coulomb interactions, and more strongly on the cage isomer, with variations of up to approximately 13 cm(-1). Analysis of the metal motions inside the cage shows that they can be chaotic. The origin of such chaotic behavior is discussed.

Modeling the stability and the motion of DNA nucleobases on the gold surface

We simulate the structure and dynamics of the four DNA bases on the most stable gold surface. The experimental adsorption energies are reproduced to about 1 kcal mol(-1), and the existence of anchor points in the molecules is evidenced. The simulations also show that the bases drift on the gold surface with a degree of mobility that is not inversely proportional to the experimental (and calculated) desorption energies. When the same type of calculations is applied to pairs of bases it is seen that for at least two of them, namely GG and TT, there is a cooperative effect that increases their adsorption energy with respect to those of the single molecules. The molecular mobility on the surface is still present when a pair of interacting bases is considered.