A Theoretical Study of the Electrochemical Gate Effect in a STM-based biomolecular transistor

ElectroChemical Scanning Tunneling Microscopy (ECSTM) is gaining popularity as a tool to implement proof-of-concept single (bio)molecular transistors. The understanding of such systems requires a discussion of the mechanism of the electrochemical current gating, which is intimately related to the electrostatic potential distribution in the tip-substrate gap where the redox active adsorbate is placed. In this article, we derive a relation that connects the local standard potential of the redox molecule in the tunneling junction with the applied electrode potentials, and we compare it with previously proposed relations. In particular, we show that a linear dependence of the local standard potential on the applied bias does not necessarily imply a monotonous potential drop between the electrodes. In addition, we calculate the electrostatic potential distribution and the parameters entering the derived relation for ECSTM on a redox metalloprotein (Azurin from P. Aeruginosa), for which experimental results exist. Finally, we give an estimate of the gating efficiency when the ECSTM setup including Azurin is interpreted as a single biomolecular wet transistor, confirming the effectiveness of the electrochemical gating for this system

Role of coherence in the plasmonic control of molecular absorption

The interpretation of nanoplasmonic effects on molecular properties, such as metal-enhanced absorption or fluorescence, typically assumes a fully coherent picture (in the quantum-mechanical sense) of the phenomena. Yet, there may be conditions where the coherent picture breaks down, and the decoherence effect should be accounted for. Using a state-of-the-art multiscale model approach able to include environment-induced dephasing, here we show that metal nanoparticle effects on the light absorption by a nearby molecule is strongly affected (even qualitatively, i.e., suppression vs enhancement) by molecular electronic decoherence. The present work shows that decoherence can be thought of as a further design element of molecular nanoplasmonic systems

Load-Induced Confinement Activates Diamond Lubrication by Water

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Photochemistry in the strong coupling regime: A trajectory surface hopping scheme

The strong coupling regime between confined light and organic molecules turned out to be promising in modifying both the ground state and the excited states properties. Under this peculiar condition, the electronic states of the molecule are mixed with the quantum states of light. The dynamical processes occurring on such hybrid states undergo several modifications accordingly. Hence, the dynamical description of chemical reactivity in polaritonic systems needs to explicitly take into account the photon degrees of freedom and nonadiabatic events. With the aim of describing photochemical polaritonic processes, in the present work, we extend the direct trajectory surface hopping scheme to investigate photochemistry under strong coupling between light and matter

Polarization dependence of emission spectra of multiexcitons in self-assembled quantum dots

We have investigated the polarization dependence of the emission spectra of p-shell multiexcitons of a quantum dot when the single particle level spacing is larger than the characteristic energy of the Coulomb interactions. We find that there are many degenerate multiexciton states. The emission intensities depend on the number of degenerate initial and final states of the optical transitions. However, unlike the transition energies, they are essentially independent of the strength of the Coulomb interactions. In the presence of electron-hole symmetry the independence is exact.Comment: 7 pages, 5 figures, published in Solid State Commu

Effective single mode methodology for strongly coupled multimode molecular-plasmon nanosystems

Strong coupling between molecules and quantized fields has emerged as an effective methodology to engineer molecular properties. New hybrid states are formed when molecules interact with quantized fields. Since the properties of these states can be modulated by fine-tuning the field features, an exciting and new side of chemistry can be explored. In particular, significant modifications of the molecular properties can be achieved in plasmonic nanocavities, where the field quantization volume is reduced to sub-nanometric volumes. Intriguing applications of nanoplasmonics include the possibility of coupling the plasmons with a single molecule, instrumental for sensing, high-resolution spectroscopy, and single-molecule imaging. In this work, we focus on phenomena where the simultaneous effects of multiple plasmonic modes are critical. We propose a theoretical methodology to account for many plasmonic modes simultaneously while retaining computational feasibility. Our approach is conceptually simple and allows us to accurately account for the multimode effects and rationalize the nature of the interaction between multiple plasmonic excitations and molecules.Comment: 27 pages, 6 figure

The interaction with gold suppresses fiber-like conformations of the amyloid beta (16-22) peptide

Inorganic surfaces and nanoparticles can accelerate or inhibit the fibrillation process of proteins and peptides, including the biomedically relevant amyloid β peptide. However, the microscopic mechanisms that determine such an effect are still poorly understood. By means of large-scale, state-of-the-art enhanced sampling molecular dynamics simulations, here we identify an interaction mechanism between the segments 16–22 of the amyloid β peptide, known to be fibrillogenic by itself, and the Au(111) surface in water that leads to the suppression of fiber-like conformations from the peptide conformational ensemble. Moreover, thanks to advanced simulation analysis techniques, we characterize the conformational selection vs. induced fit nature of the gold effect. Our results disclose an inhibition mechanism that is rooted in the details of the microscopic peptide–surface interaction rather than in general phenomena such as peptide sequestration from the solution.ISSN:2040-3364ISSN:2040-337

The Conformational Dynamics of the Ligands Determines the Electronic Circular Dichroism of the Chiral Au38(SC2H4Ph)24 Cluster

Effects of the conformational dynamics of 2-PET protective ligands on the electronic circular dichroism (ECD) of the chiral Au-38(SC2H4Ph)(24) cluster are investigated. We adopt a computational protocol in which ECD spectra are calculated via the first principle polTDDFT approach on a series of conformations extracted from MD simulations by using Essential Dynamics (ED) analysis, and then properly weighted to predict the final spectrum. We find that the experimental spectral features are well reproduced, whereas significant discrepancies arise when the spectrum is calculated using the experimental X-ray structure. This result unambiguously demonstrates the need to account for the conformational effects in the ECD modeling of chiral nanoclusters. The present procedure proved to be able of capturing the essential conformational features of the dynamic Au-38(SC2H4Ph)(24) system, opening the possibility to model the ECD of soluble chiral nanoclusters in a realistic way

Simulating Plasmon Resonances of Gold Nanoparticles with Bipyramidal Shapes by Boundary Element Methods

Computational modeling and accurate simulations of localized surface plasmon resonance (LSPR) absorption properties are reported for gold nanobipyramids (GNBs), a class of metal nanoparticle that features highly tunable, geometry-dependent optical properties. GNB bicone models with spherical tips performed best in reproducing experimental LSPR spectra while the comparison with other geometrical models provided a fundamental understanding of base shapes and tip effects on the optical properties of GNBs. Our results demonstrated the importance of averaging all geometrical parameters determined from transmission electron microscopy images to build representative models of GNBs. By assessing the performances of LSPR absorption spectra simulations based on a quasi-static approximation, we provided an applicability range of this approach as a function of the nanoparticle size, paving the way to the theoretical study of the coupling between molecular electron densities and metal nanoparticles in GNB-based nanohybrid systems, with potential applications in the design of nanomaterials for bioimaging, optics and photocatalysis