Spectroscopic Tracking of Molecular Transport Junctions Generated by Using Click Chemistry

Click to fill the gap : The in situ modular fabrication of molecular transport junctions in nanogaps generated by on‐wire lithography is achieved by using click chemistry (see picture). The formation of molecular junctions proceeds in high yields and can be used to test different molecules; the triazole group also maintains conjugation in the molecular wires. Raman spectroscopy is used to characterize the molecular assembly processes.

     

Propensity rules for inelastic electron tunneling spectroscopy of single-molecule transport junctions

Using a perturbative approach to simple model systems, we derive useful propensity rules for inelastic electron tunneling spectroscopy (IETS) of molecular wire junctions. We examine the circumstances under which this spectroscopy (that has no rigorous selection rules) obeys well defined propensity rules based on the molecular symmetry and on the topology of the molecule in the junction. Focusing on conjugated molecules of C(2h) symmetry, semiquantitative arguments suggest that the IETS is dominated by a(g) vibrations in the high energy region and by out of plane modes (a(u) and b(g)) in the low energy region. Realistic computations verify that the proposed propensity rules are strictly obeyed by medium to large-sized conjugated molecules but are subject to some exceptions when small molecules are considered. The propensity rules facilitate the use of IETS to help characterize the molecular geometry within the junction.     

Ion current calculations based on three dimensional Poisson-Nernst-Planck theory for a cyclic peptide nanotube

Ion current calculations based on Poisson-Nernst-Planck (PNP) theory are performed for a synthetic cyclic peptide nanotube that consists of eight or ten cyclo[(-L-Trp-D-Leu-)4] embedded in a lipid bilayer membrane to investigate the ion transport properties of the nanotube. To explore systems with arbitrary geometries, three-dimensional PNP theory is implemented using a finite difference method. The influence of dipolar lipid molecules on the ion currents is also examined by turning on or off the charges of the lipid dipoles in dipalmitoylphosphatidylcholine (DPPC). Comparisons between the calculated and experimentally measured ion currents show that the PNP approach agrees well with the measurements at low ion concentrations but overestimates the currents at higher concentrations. Concentration profiles reveal the selectivity of the peptide nanotube to cations, which is attributed to the negatively charged carbonyl oxygens inside the nanotube. The dominant cation and the minimum anion concentrations inside the cyclic peptide nanotube suggest that these cyclic peptide nanotubes can be employed as ion sensors. In the case of the polar DPPC bilayer, smaller currents are obtained in the calculation. The variation of current with polarity of the lipids implies that both polar and nonpolar lipid bilayer membranes can be utilized to regulate ion currents in the peptide nanotube and other ion channels. Strengths and limitations of the PNP theory are also discussed.     

Electron transfer in multiply bridged donor-acceptor molecules: Dephasing and quantum coherence

We present a simple theoretical treatment of nonadiabatic electron transfer in multiply bridged donor-bridge-acceptor molecules using the density matrix formalism. Destructive interference can result from different signed couplings between bridge sites, with the simplest system being a four-site Joachim-type molecular interferometer. Previous work has shown that deposition of energy on the bridge sites erases the interference and recovers transport. We show that pure local dephasing, a completely elastic process, is also capable of eliminating destructive interference and regaining transport. Destructive interference as a result of system connectivity can explain the familiar ortho-meta-para reactivity of benzene bridges. We also show that pure dephasing can yield a coalescence of ortho, meta, and para effective coupling strengths and suggest a system to observe this effect experimentally.     

Atomic-scale roughness effect on capillary force in atomic force microscopy

We study the capillary force in atomic force microscopy by using Monte Carlo simulations. Adopting a lattice gas model for water, we simulated water menisci that form between a rough silicon-nitride tip and a mica surface. Unlike its macroscopic counterpart, the water meniscus at the nanoscale gives rise to a capillary force that responds sensitively to the tip roughness. With only a slight change in tip shape, the pull-off force significantly changes its qualitative variation with humidity.     

Photochromism of side-chain liquid crystal polymers containing spironaphthoxazines

Side-chain liquid crystal polyacrylates and polysiloxanes containing different photochromic spironaphthoxazine side groups were synthesized. Thermodynamic, spectral and kinetic properties of the polymers were investigated. The structure of the mesophase is discussed.     

On the role of nuclear motions in electron and excitation transfer rates: Importance of transfer-integral dependence upon nuclear coordinate

The role of nuclear degrees of freedom in modifying the electron or exciton transfer rates between molecules is investigated. In addition to the usual Franck-Condon overlap factors which arise from the overlaps of initial and final vibrational states, we discuss a dependence of the transfer integral upon nuclear motions, a dependence which has been often cited, but nearly always ignored, in the usual dynamical theories of transfer processes. We show, within a Bom-Oppenheimer treatment, that the transfer integral dependence upon librational, rotational and vibrational modes can profoundly change both the rate itself and its functional dependences (upon temperature, upon orientation, etc.). Using a simple cosine form for the dependence of the transfer integral upon the modifying nuclear mode and a simple displaced-oscillator transformation, we obtain a closed-form solution for the transfer rate, which includes a new overlap factor arising from the dependence of the transfer integral upon nuclear coordinates. Some general remarks about the role of this dependence are made, and applications to particular transfer systems are briefly discussed.