Agostino Migliore

Covalently bonded single-molecule junctions with stable and reversible photoswitched conductivity

Stable molecular switches Many single-molecule current switches have been reported, but most show poor stability because of weak contacts to metal electrodes. Jia et al. covalently bonded a diarylethene molecule to graphene electrodes and achieved stable photoswitching at room temperature (see the Perspective by Frisbie). The incorporation of short bridging alkyl chains between the molecule and graphene decoupled their pielectron systems and allowed fast conversion of the open and closed ring states. Science, this issue p. 1443; see also p. 1394 Stable molecular conduction junctions were formed by covalently bonding single diarylethenes to graphene electrodes. Through molecular engineering, single diarylethenes were covalently sandwiched between graphene electrodes to form stable molecular conduction junctions. Our experimental and theoretical studies of these junctions consistently show and interpret reversible conductance photoswitching at room temperature and stochastic switching between different conductive states at low temperature at a single-molecule level. We demonstrate a fully reversible, two-mode, single-molecule electrical switch with unprecedented levels of accuracy (on/off ratio of ~100), stability (over a year), and reproducibility (46 devices with more than 100 cycles for photoswitching and ~105 to 106 cycles for stochastic switching).

Biochemistry and Theory of Proton-Coupled Electron Transfer

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Long-range charge transport in single G-quadruplex DNA molecules

DNA and DNA-based polymers are of interest in molecular electronics because of their versatile and programmable structures. However, transport measurements have produced a range of seemingly contradictory results due to differences in the measured molecules and experimental set-ups, and transporting significant current through individual DNA-based molecules remains a considerable challenge. Here, we report reproducible charge transport in guanine-quadruplex (G4) DNA molecules adsorbed on a mica substrate. Currents ranging from tens of picoamperes to more than 100 pA were measured in the G4-DNA over distances ranging from tens of nanometres to more than 100 nm. Our experimental results, combined with theoretical modelling, suggest that transport occurs via a thermally activated long-range hopping between multi-tetrad segments of DNA. These results could re-ignite interest in DNA-based wires and devices, and in the use of such systems in the development of programmable circuits.

Charge transfer in dynamical biosystems, or the treachery of (static) images.

Conspectus The image is not the thing. Just as a pipe rendered in an oil painting cannot be smoked, quantum mechanical coupling pathways rendered on LCDs do not convey electrons. The aim of this Account is to examine some of our recent discoveries regarding biological electron transfer (ET) and transport mechanisms that emerge when one moves beyond treacherous static views to dynamical frameworks. Studies over the last two decades introduced both atomistic detail and macromolecule dynamics to the description of biological ET. The first model to move beyond the structureless square-barrier tunneling description is the Pathway model, which predicts how protein secondary motifs and folding-induced through-bond and through-space tunneling gaps influence kinetics. Explicit electronic structure theory is applied routinely now to elucidate ET mechanisms, to capture pathway interferences, and to treat redox cofactor electronic structure effects. Importantly, structural sampling of proteins provides an understanding of how dynamics may change the mechanisms of biological ET, as ET rates are exponentially sensitive to structure. Does protein motion average out tunneling pathways? Do conformational fluctuations gate biological ET? Are transient multistate resonances produced by energy gap fluctuations? These questions are becoming accessible as the static view of biological ET recedes and dynamical viewpoints take center stage. This Account introduces ET reactions at the core of bioenergetics, summarizes our team’s progress toward arriving at an atomistic-level description, examines how thermal fluctuations influence ET, presents metrics that characterize dynamical effects on ET, and discusses applications in very long (micrometer scale) bacterial nanowires. The persistence of structural effects on the ET rates in the face of thermal fluctuations is considered. Finally, the flickering resonance (FR) view of charge transfer is presented to examine how fluctuations control low-barrier transport among multiple groups in van der Waals contact. FR produces exponential distance dependence in the absence of tunneling; the exponential character emerges from the probability of matching multiple vibronically broadened electronic energies within a tolerance defined by the rms coupling among interacting groups. FR thus produces band like coherent transport on the nanometer length scale, enabled by conformational fluctuations. Taken as a whole, the emerging context for ET in dynamical biomolecules provides a robust framework to design and interpret the inner workings of bioenergetics from the molecular to the cellular scale and beyond, with applications in biomedicine, biocatalysis, and energy science.

Nonlinear charge transport in redox molecular junctions: a Marcus perspective.

Redox molecular junctions are molecular conduction junctions that involve more than one oxidation state of the molecular bridge. This property is derived from the ability of the molecule to transiently localize transmitting electrons, implying relatively weak molecule-leads coupling and, in many cases, the validity of the Marcus theory of electron transfer. Here we study the implications of this property on the nonlinear transport properties of such junctions. We obtain an analytical solution of the integral equations that describe molecular conduction in the Marcus kinetic regime and use it in different physical limits to predict some important features of nonlinear transport in metal-molecule-metal junctions. In particular, conduction, rectification, and negative differential resistance can be obtained in different regimes of interplay between two different conduction channels associated with different localization properties of the excess molecular charge, without specific assumptions about the electronic structure of the molecular bridge. The predicted behaviors show temperature dependences typically observed in the experiment. The validity of the proposed model and ways to test its predictions and implement the implied control strategies are discussed.

First Principles Effective Electronic Couplings for Hole Transfer in Natural and Size-Expanded DNA

Hole transfer processes between base pairs in natural DNA and size-expanded DNA (xDNA) are studied and compared, by means of an accurate first principles evaluation of the effective electronic couplings (also known as transfer integrals), in order to assess the effect of the base augmentation on the efficiency of charge transport through double-stranded DNA. According to our results, the size expansion increases the average electronic coupling, and thus the CT rate, with potential implications in molecular biology and in the implementation of molecular nanoelectronics. Our analysis shows that the effect of the nucleobase expansion on the charge-transfer (CT) rate is sensitive to the sequence of base pairs. Furthermore, we find that conformational variability is an important factor for the modulation of the CT rate. From a theoretical point of view, this work offers a contribution to the CT chemistry in pi-stacked arrays. Indeed, we compare our methodology against other standard computational frameworks that have been adopted to tackle the problem of CT in DNA, and unravel basic principles that should be accounted for in selecting an appropriate theoretical level.

Nonorthogonality Problem and Effective Electronic Coupling Calculation: Application to Charge Transfer in π-Stacks Relevant to Biochemistry and Molecular Electronics

A recently proposed method for the calculation of the effective electronic coupling (or charge-transfer integral) in a two-state system is discussed and related to other methods in the literature. The theoretical expression of the coupling is exact within the two-state model and applies to the general case where the charge transfer (CT) process involves nonorthogonal initial and final diabatic (localized) states. In this work, it is shown how this effective electronic coupling is also the one to be used in a suitable extension of Rabis formula to the nonorthogonal representation of two-state dynamical problems. The formula for the transfer integral is inspected in the regime of long-range CT and applied to CT reactions in redox molecular systems of interest to biochemistry and/or to molecular electronics: the guanine-thymine stack from regular B-DNA, the polyaromatic perylenediimide stack, and the quinol-semiquinone couple. The calculations are performed within the framework of the Density Functional Theory (DFT), using hybrid exchange-correlation (XC) density functionals, which also allowed investigation of the appropriateness of such hybrid-DFT methods for computing electronic couplings. The use of the recently developed M06-2X and M06-HF density functionals in appropriate ways is supported by the results of this work.

First-principles density-functional theory calculations of electron-transfer rates in azurin dimers

We have conceived and implemented a new method to calculate transfer integrals between molecular sites, which exploits few quantities derived from density-functional theory electronic structure computations and does not require the knowledge of the exact transition state coordinate. The method uses a complete multielectron scheme, thus including electronic relaxation effects. Moreover, it makes no use of empirical parameters. The computed electronic couplings can then be combined with estimates of the reorganization energy to evaluate electron-transfer rates that are measured in kinetic experiments: the latter are the basis to interpret electron-transfer mechanisms. We have applied our approach to the study of the electron self-exchange reaction of azurin, an electron-transfer protein belonging to the family of cupredoxins. The transfer integral estimates provided by the proposed method have been compared with those resulting from other computational techniques, from empirical models, and with available experimental data.

Full-electron calculation of effective electronic couplings and excitation energies of charge transfer states: Application to hole transfer in DNA π-stacks

In this work I develop and apply a theoretical method for calculating effective electronic couplings (or transfer integrals) between redox sites involved in hole or electron transfer reactions. The resulting methodology is a refinement and a generalization of a recently developed approach for transfer integral evaluation. In fact, it holds for any overlap between the charge-localized states used to represent charge transfer (CT) processes in the two-state model. The presented theoretical and computational analyses show that the prototype approach is recovered for sufficiently small overlaps. The method does not involve any empirical parameter. It allows a complete multielectron description, therefore including electronic relaxation effects. Furthermore, its theoretical formulation holds at any value of the given reaction coordinate and yields a formula for the evaluation of the vertical excitation energy (i.e., the energy difference between the adiabatic ground and first-excited electronic states) that rests on the same physical quantities used in transfer integral calculation. In this paper the theoretical approach is applied to CT in B-DNA base dimers within the framework of Density Functional Theory (DFT), although it can be implemented in other computational schemes. The results of this work, as compared with previous Hartree-Fock (HF) and post-HF evaluations, support the applicability of the current implementation of the method to larger pi-stacked arrays, where post-HF approaches are computationally unfeasible.

Quantum Mechanical and Quantum Mechanical/Molecular Mechanical Studies of the Iron−Dioxygen Intermediates and Proton Transfer in Superoxide Reductase

Classical and quantum-chemical computations are employed to probe the reaction intermediates and proton-transfer processes in superoxide reductase (SOR) from Desulfoarculus baarsii. Ab initio studies of the SOR active site, as well as classical and QM/MM MD simulations on the overall enzymatic reaction, are performed. We explore the use of a Hubbard U correction to standard density functional theory (DFT) in order to obtain a better description of the strongly correlated d electrons in the transition-metal center. The results obtained from the standard and Hubbard-U-corrected DFT approaches are compared with those obtained using different hybrid-DFT functionals. We show that the Hubbard U correction gives a significant improvement in the description of the structural, energetic, and electronic properties of SOR. We establish that adopting the Hubbard U correction in the QM/MM approach leads to increased accuracy with essentially no additional computational cost. Our results suggest that Lys(48) is one of the likely sources of the first proton donation to the superoxide, either directly or through an interstitial water molecule. Our QM/MM calculations highlight the important role of the interactions and hydrogen-bond network created by the imidazole rings of the His ligands and the internal water molecules. Whereas the hydrogen-bonding pattern due to internal waters can facilitate the protonation event, the interactions with the His ligands and the hydrogen bonds with water can stabilize the dioxygen ligand in a side-on conformation, which, in turn, prevents the immediate proton transfer from Lys(48), as indicated by recent experimental studies.