Can a synthetic thread act as an electrochemically switchable molecular device?

On the supramolecular interactions into a pH- and Metal-Actuated Molecular Shuttle: some insights from QTAIM modeling

Supramolecular contacts responsible for chemical interaction of cucurbit[7]uril (CB[7]) macrocycle on a Tolyl-Viologen-Phenylene-Imidazole (T-VPI) molecular thread, at acid pH (T-VPI-H+) or after Ag+ cation addition (T-VPI-Ag+), are analytically addressed in a computational framework combining Quantum Theory of Atoms in Molecules (QTAIM) with Density Functional Theory (DFT). In this respect, the crystallographic structure (CCDC number 2217466) is taken as reference condition for addressing the nature of the chemical interactions driving the shuttling of the CB[7] between T and P stations recently observed in dilute water solutions. Beside the host(CB[7]) vs guest(T-VPI-H+ or T-VPI-Ag+) complexation, the coordination sphere of the Ag+ cation is also investigated by means of local electronic energy density - H(r) - descriptors. The derived non-covalent interaction patterns are found to support diagnostic 1H NMR signals used for detecting the mutual position of the CB[7] along the axle. This work highlights the potentialities of a QTAIM based approach in the characterization of supramolecular and metal-complexation effects in molecular aggregates such as not-interlocked synthetic molecular shuttles.

A computational study of a light-driven artificial device: a third generation rotational photo-molecular motor in dilute solutions

A third-generation artificial photo-molecular motor, featuring two photo-switchable rotating moieties in connection with a pseudoasymmetric molecular centre, is investigated by combining quantum-mechanics (QM) algorithms with classical molecular dynamics (MD) propagators. In particular, in the present contribution we have addressed such a molecular motor in different rotational isomers following the experimental observations arising from the application of multiple spectroscopic techniques in dilute solutions. At first, we focused our attention on the reproduction of the UV/Vis absorption spectrum in two solvents (acetonitrile and cyclohexane) with different gradient-corrected density functional theory (B3LYP, Cam-B3LYP, PBE, PBE0) functionals in conjunction with the conductor-like and polarizable continuum model (C-PCM). Furthermore, we refined the absorption signals by combining a classical MD sampling at room-temperature with DFT-based electronic degrees of freedom to compute perturbed excitation wavelengths driven by thermal fluctuation and solvation effects. In this respect, we have modelled the investigated artificial motor within solution nanodroplets with solvent molecules treated contextually at atomistic level and via a dielectric and polarizable continuum model.

Copper(II) Coordination and Translocation in Luteolin and Effect on Radical Scavenging

Luteolin differs as a radical scavenger dramatically from apigenin in response to Cu(II) coordination despite a minor structural difference. Coordination of Cu(II) increases the radical scavenging efficiency of luteolin, especially at low pH, while decreases the efficiency of apigenin at both low and higher pH as studied by ABTS^•+ radical scavenging. Luteolin forms a 1:1 complex with Cu(II) binding to 4-carbonyl and 5-phenol for pH <6 and to 3',4'-catechol for pH >6. Apigenin forms a 1:2 complex independent of pH coordinated to 4-carbonyl and 5-hydroxylyl. Cu(II) coordinated to luteolin, as studied by pH jump stopped-flow, translocates with rate constants of 11.1 ± 0.3 s^-1 from 4,5 to 3',4' sites and 1.0 ± 0.1 s^-1 from 3',4' to 4,5 sites independent of Cu(II) concentration, pointing toward the dissociation of Cu(II) from an intermediate with two Cu(II) coordination as rate determining. 3',4'-Catechol is suggested to be a switch for Cu(II) translocation with deprotonation initiating 4,5 to 3',4' translocation and protonation initiating 3',4' to 4,5 translocation. For dicoordinated apigenin, the coordination symmetry balances an electron withdrawal effect of Cu(II) resulting in a decrease of phenol acidity and less radical scavenging efficiency compared to parent apigenin. Compared to that of parent luteolin, the radical scavenging rate of both 4,5 and 3',4' Cu(II)-coordinated luteolin is enhanced through increased phenol acidity by electron withdrawal by Cu(II), as confirmed by density functional theory (DFT) calculations. Coordination and translocation of Cu(II) accordingly increases the antioxidant activity of luteolin at pH approaching the physiological level and is discovered as a novel class of natural molecular machinery derived from plant polyphenols, which seems to be of importance for protection against oxidative stress.

Charge transfer equilibria of aqueous single stranded DNA

The charge transfer thermodynamics of a simple model of DNA, a single stranded 10-mer poly-adenine oligonucleotide, in water is investigated by means of a computational/theoretical procedure, in which all the relevant environmental effects are considered. Our data indicate that water and counterions ultimately dominate the DNA reduction and oxidation free energies, which are also strongly influenced by the base position along the strand. In fact, we estimated that reduction free energies are large and negative, particularly for the bases close to the 5' and 3' positions, whereas the electron detachment is thermodynamically unfavoured all along the strand, but with a higher free energy cost in the central region of the molecule. Further investigation on double charging, i.e. one nucleobase is oxidized and one is reduced within the strand, predicts that charge-separated states are possible and thermodynamically largely stable when the ionic forms are separated by several nucleobases.