Molecular recognition of DNA by rigid [n]-polynorbornane-derived bifunctional intercalators: synthesis and evaluation of their binding properties

We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27 and a binding constant of about 8 M. 9-Aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding.

Extending distannoxane double ladders using rigid spacers: a double ladder with eight chiral tin atoms-and a twist!

The new bulky silicon-containing ditin precursor p-(RCl₂SnCH₂SiMe₂)₂C₆H₄ (R = CH₂SiMe₃ (4)) has been synthesized and further reacted to form a unique double ladder {[p-(R(Cl)SnCH₂SiMe₂)₂C₆H₄]O}₄ (6). The two layers within 6 are twisted with respect to one another, resulting in a helical motif and a total absence of molecular symmetry so that there are eight chiral tin atoms within the system. The structure is compared to the double ladder {[m-(R(Cl)SnCH₂CH₂)₂C₆H₄]O}₄ (11), which was prepared from the less sterically demanding ditin precursor m-(RCl₂SnCH₂CH₂)₂C₆H₄ (10). The two layers within 11 are parallel, and the molecule contains only two kinds of tin atom.

Single molecule conductance through rigid norbornylogous bridges with zero average curvature

A new homologous series of norbornylogous (NB) bridges has been synthesized in which the average curvature of the bridges is very small. The molecules are rigid and have two thiol moieties at each end to allow them to form self-assembled monolayers (SAMs) and to connect to two gold electrodes to form a molecular junction. The SAMs formed were characterized using electrochemistry to determine the surface coverage of molecules on gold surface and to provide an indication of the packing of the NB bridges while ellipsometry and X-ray photoelectron spectroscopy (XPS) were used to provide an indication of the SAM thickness and orientation. Single molecule conductance of NB bridges was measured as a function of the molecular length. The conductance was found to decrease exponentially with the length with a decay constant that is exactly correlated with photoelectron transfer and other studies at the multiple molecule level. The molecule−electrode contact resistance was determined and compared with that of related alkanedithiol molecular junctions.

Polymer architecture effect on sodium ion transport in PSTFSI-based ionomers: a molecular dynamics study

In this study, we investigated the effect of polymer architecture on the ion dynamics and local structure to understand the factors that might lead to the design of highly conductive and mechanically robust polyelectrolytes. Molecular dynamic simulations were undertaken on the sodium poly[(4-styrenesulfonyl) (trifluoromethanesulfonyl) imide] P(STFSINa) homopolymer and its copolymers with either ether or styrene spacer groups to investigate the spacer length and polarity dependence of Na-ion transport. Using a scaled charge model, we observed a continuous ion aggregate network in the homopolymer, which facilitates the fast ion dynamics despite the rigid polymer matrix. The longest spacer groups disrupt this percolating ionic network differently, with the ether group being more disruptive than the styrene group, and leading to more discrete ionic aggregates. The copolymer with the ether spacer was also found to result in an alternative Na-ion diffusion mechanism.

Molecular dynamics study of a dual-cation ionomer electrolyte

The poly(N1222)xLi1-x[AMPS] ionomer system with dual cations has previously shown decoupled Li ion dynamics from polymer segmental motions, characterized by the glass transition temperature, which can result in a conductive electrolyte material whilst retaining an appropriate modulus (ie. stiffness) so that it can suppress dendrite formation, thereby improving safety when used in lithium metal batteries. To understand this ion dynamics behavior, molecular dynamics techniques have been used in this work to simulate structure and dynamics in these materials. These simulations confirm that the Li ion transport is decoupled from the polymer particularly at intermediate N1222+ concentrations. At 50 mol% N1222+ concentration the polymer backbone is more rigid than for higher N1222+ concentrations, but with increasing temperature Li ion transport is more significant than polymer or quaternary ammonium cation motions. Here we suggest an ion hopping mechanism for Li+, arising from structural rearrangement of ionic clusters that could explain its decoupled behavior. Higher temperatures favor an aggregated ionic structure as well as enhancing these hopping motions. The simulations discussed here provide an atomic-level understanding of ion dynamics that could contribute to designing an improved ionomer with fast ion transport and mechanical robustness.