Stretching-induced conductance variations as fingerprints of contact configurations in single-molecule junctions

Molecule-electrode contact atomic structures are a critical factor that characterizes molecular devices, but their precise understanding and control still remain elusive. Based on combined first-principles calculations and single-molecule break junction experiments, we herein establish that the conductance of alkanedithiolate junctions can both increase and decrease with mechanical stretching and the specific trend is determined by the S-Au linkage coordination number (CN) or the molecule-electrode contact atomic structure. Specifically, we find that the mechanical pulling results in the conductance increase for the junctions based on S-Au CN two and CN three contacts, while the conductance is minimally affected by stretching for junctions with the CN one contact and decreases upon the formation of Au monoatomic chains. Detailed analysis unravels the mechanisms involving the competition between the stretching-induced upshift of the highest occupied molecular orbital-related states toward the Fermi level of electrodes and the deterioration of molecule-electrode electronic couplings in different contact CN cases. Moreover, we experimentally find a higher chance to observe the conductance enhancement mode under a faster elongation speed, which is explained by ab initio molecular dynamics simulations that reveal an important role of thermal fluctuations in aiding deformations of contacts into low-coordination configurations that include monoatomic Au chains. Pointing out the insufficiency in previous notions of associating peak values in conductance histograms with specific contact atomic structures, this work resolves the controversy on the origins of ubiquitous multiple conductance peaks in S-Au-based single-molecule junctions.Comment: 11 pages, 4 figures; to be published in J. Am. Chem. So

Ionic Signal Amplification of DNA in a Nanopore

Ionic signal amplification is a key challenge for single-molecule analyses by solid-state nanopore sensing. Here, a permittivity gradient approach for amplifying ionic blockade characteristics of DNA in a nanofluidic channel is reported. The transmembrane ionic current response is found to change substantially through modifying the liquid permittivity at one side of a pore with an organic solvent. Imposing positive liquid permittivity gradients with respect to the direction of DNA electrophoresis, this study observes the resistive ionic signals to become larger due to the varying contributions of molecular counterions. On the contrary, negative gradients render adverse effects causing conductive ionic current pulses upon polynucleotide translocations. Most importantly, both the positive and negative gradients are demonstrated to be capable of amplifying the ionic signals by an order of magnitude with a 1.3-fold difference in the transmembrane liquid dielectric constants. This phenomenon allows a novel way to enhance the single-molecule sensitivity of nanopore sensing that may be useful in analyzing secondary structures and genome sequence of DNA by ionic current measurements.This is the pre-peer reviewed version of the following article: Tsutsui, M., Yokota, K., He, Y., Kawai, T., Ionic Signal Amplification of DNA in a Nanopore. Small Methods 2022, 6, 2200761, which has been published in final form at https://doi.org/10.1002/smtd.202200761. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving

Electrochemical response of biased nanoelectrodes in solution

Novel approaches to DNA sequencing and detection require the measurement of electrical currents between metal probes immersed in ionic solution. Here, we experimentally demonstrate that these systems maintain large background currents with a transient response that decays very slowly in time and noise that increases with ionic concentration. Using a non-equilibrium stochastic model, we obtain an analytical expression for the ionic current that shows these results are due to a fast electrochemical reaction at the electrode surface followed by the slow formation of a diffusion layer. During the latter, ions translocate in the weak electric field generated after the initial rapid screening of the strong fields near the electrode surfaces. Our theoretical results are in very good agreement with experimental findings

Enhanced Nanoparticle Sensing in a Highly Viscous Nanopore

Kawaguchi T., Tsutsui M., Murayama S., et al. Enhanced Nanoparticle Sensing in a Highly Viscous Nanopore. Small Methods , (2024); https://doi.org/10.1002/smtd.202301523.Slowing down translocation dynamics is a crucial challenge in nanopore sensing of small molecules and particles. Here, it is reported on nanoparticle motion-mediated local viscosity enhancement of water-organic mixtures in a nanofluidic channel that enables slow translocation speed, enhanced capture efficiency, and improved signal-to-noise ratio by transmembrane voltage control. It is found that higher detection rates of nanoparticles under larger electrophoretic voltage in the highly viscous solvents. Meanwhile, the strongly pulled particles distort the liquid in the pore at high shear rates over 103 s−1 which leads to a counterintuitive phenomenon of slower translocation speed under higher voltage via the induced dilatant viscosity behavior. This mechanism is demonstrated as feasible with a variety of organic molecules, including glycerol, xanthan gum, and polyethylene glycol. The present findings can be useful in resistive pulse analyses of nanoscale objects such as viruses and proteins by allowing a simple and effective way for translocation slowdown, improved detection throughput, and enhanced signal-to-noise ratio

Modular Plasmonic Nanopore for Opto‐Thermal Gating

Solid-state nanopore gating inspired by biological ion channels is gaining increasing traction due to a large range of applications in biosensing and drug delivery. Integration of stimuli-responsive molecules such as poly(N-isopropylacrylamide) (PNIPAM) inside nanopores can enable temperature-dependent gating, which so far has only been demonstrated using external heaters. In this work, plasmonic resonators are combined inside the nanopore architecture with PNIPAM to enable optical gating of individual or multiple nanopores with micrometer resolution and a switching speed of a few milliseconds by thermo-plasmonics effects. A temperature change of 40 kelvin per millisecond is achieved and demonstrates the efficacy of this method using nanopore ionic conductivity measurements that enable selective activation of individual nanopores in an array. Moreover, the selective gating of specific nanopores in an array can set distinct ionic conductance levels: low, medium, and high (i.e., “0,” “1,” and “2”), which can be exploited for logical gating with optical signal control. Such selective optical gating in nanopore arrays marks a breakthrough in nanofluidics, as it paves the way toward smart devices that offer multifunctional applications including biosensing, targeted drug delivery, and fluidic mixing.CHEMIN

Modular plasmonic nanopore for opto-thermal gating

Solid-state nanopore gating inspired by biological ion channels is gaining increasing traction due to a large range of applications in biosensing and drug delivery. Integration of stimuli-responsive molecules such as poly(N-isopropylacrylamide) (PNIPAM) inside nanopores can enable temperature-dependent gating, which so far has only been demonstrated using external heaters. In this work, we combine plasmonic resonators inside the nanopore architecture with PNIPAM to enable optical gating of individual or multiple nanopores with micrometer resolution and a switching speed of few milliseconds by thermo-plasmonics. We achieve a temperature change of 40 kelvin per millisecond and demonstrate the efficacy of this method using nanopore ionic conductivity measurements that enables selective activation of individual nanopores in an array. Moreover, the selective gating of specific nanopores in an array can set distinct ionic conductance levels: low, medium, and high (i.e., 0, 1, and 2), which could be exploited for logical gating with optical signal control. Such selective optical gating in nanopore arrays marks a breakthrough in nanofluidics, as it paves the way towards smart devices that offer multifunctional applications including biosensing, targeted drug delivery, and fluidic mixing

MCBJ ギホウ オ モチイタ ゲンシ ブンシ ドウデンタイ ノ デンシ デンドウ ニ カンスル ケンキュウ

京都大学0048新制・課程博士博士(工学)甲第12324号工博第2653号新制||工||1375(附属図書館)24160UT51-2006-J316京都大学大学院工学研究科材料工学専攻(主査)教授 酒井 明, 教授 杉村 博之, 教授 松重 和美学位規則第4条第1項該当Doctor of EngineeringKyoto UniversityDA