No abstract

For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.

Nucleobases (adenine (A), thymine (T), cytosine (C), and guanine (G)) trapped within two metal clusters such as Au(3) undergo expansion. Our investigation reveals that this primarily arises due to the concomitant increase in all the bond lengths in molecules. Such expansion of the molecules can be qualitatively understood on the basis of classical harmonic potentials in the bonds and loss of aromaticity in the rings. Specifically, the highly electronegative O and N elements in the base pairs anchor to Au atoms and form X-Au bonds, which leads to charge redistribution within the molecules. As a very important consequence of this, the nature of the hydrogen bonds (in Au(3)-A...T-Au(3) and in Au(3)-G...C-Au(3)) change substantially within these electrodes in comparison to gas-phase structures. These hydrogen bonds have a single-well potential energy profile (of the type N...H...O and N...H...N) instead of double-well potentials (like N-H...O or N-H...N/ N...H-N types). A detailed energy calculation along the proton movement pathway supports our conclusions.

Density functional theory is used to reconcile the structural, magnetic and electron transport properties of a triruthenium extended metal atom chain, Ru 3 (dpa) 4 (NCS) 2 . The distinct bending of the Ru-Ru-Ru core in this species is traced to strong second-order mixing between levels of s and p symmetry that are near degenerate in the linear geometry. The dominant electron transport channel is formed by the LUMO, an orbital of p* symmetry that lies just above the Fermi level of the gold electrode. The bending has a substantial impact on electron transport in that it induces a spin crossover from a quintet to a singlet which in turn brings the LUMO much closer to the Fermi level. The presence of significant net p bonding in the metal chains also broadens the p/p nb /p* manifold, such that the channel is not strongly perturbed by the electric field, even at a bias of 1.0 V. The presence of a robust p symmetry conduction channel marks the triruthenium systems out as quite distinct from its first-row counterparts, Cr 3 (dpa) 4 (NCS) 2 and Co 3 (dpa) 4 (NCS) 2 , where current flows primarily through the s framework.

Structure and bonding for a series of oxo-bridged and sulphur bridged alkali-metal centers (M-X-M: Li, Na and K; X = O, S) are studied for various M-X-M angles. The structures for these charge-transfer systems are compared with H-X-H. These charge-transfer systems show bonding and structures that are distinctively different from the covalent H-X-H molecules. The singlet-triplet gap for all of these molecules are positive suggesting the stabilization of the spin-paired configuration instead of the paramagnetic state. The variation in the exchange-coupling constant (J) with the change in M-X-M angle suggest that the singlet-triplet gap for these systems can be reduced through stabilization of geometries with M-X-M angles differing from the ground state geometries. Strategies are proposed for reducing the singlet-triplet gaps in these systems by confining them inside fullerenes.