The Mesoscopic Electrochemistry of Molecular Junctions

Introducing Nanoscale Electrochemistry in Small-Molecule Detection for Tackling Existing Limitations of Affinity-Based Label-Free Biosensing Applications

Electrochemical sensing techniques for small molecules have progressed in many applications, including disease diagnosis and prevention as well as monitoring of health conditions. However, affinity-based detection for low-abundance small molecules is still challenging due to the imbalance in target-to-receptor size ratio as well as the lack of a highly sensitive signal transducing method. Herein, we introduced nanoscale electrochemistry in affinity-based small molecule detection by measuring the change of quantum electrochemical properties with a nanoscale artificial receptor upon binding. We prepared a nanoscale molecularly imprinted composite polymer (MICP) for cortisol by electrochemically copolymerizing β-cyclodextrin and redox-active methylene blue to offer a high target-to-receptor size ratio, thus realizing "bind-and-read" detection of cortisol as a representative target small molecule, along with extremely high sensitivity. Using the quantum conductance measurement, the present MICP-based sensor can detect cortisol from 1.00 × 10-12 to 1.00 × 10-6 M with a detection limit of 3.93 × 10-13 M (S/N = 3), which is much lower than those obtained with other electrochemical methods. Moreover, the present MICP-based cortisol sensor exhibited reversible cortisol sensing capability through a simple electrochemical regeneration process without cumbersome steps of washing and solution change, which enables "continuous detection". In situ detection of cortisol in human saliva following circadian rhythm was carried out with the present MICP-based cortisol sensor, and the results were validated with the LC-MS/MS method. Consequently, this present cortisol sensor based on nanoscale MICP and quantum electrochemistry overcomes the limitations of affinity-based biosensors, opening up new possibilities for sensor applications in point-of-care and wearable healthcare devices.

Learning Conductance: Gaussian Process Regression for Molecular Electronics

Experimental studies of charge transport through single molecules often rely on break junction setups, where molecular junctions are repeatedly formed and broken while measuring the conductance, leading to a statistical distribution of conductance values. Modeling this experimental situation and the resulting conductance histograms is challenging for theoretical methods, as computations need to capture structural changes in experiments, including the statistics of junction formation and rupture. This type of extensive structural sampling implies that even when evaluating conductance from computationally efficient electronic structure methods, which typically are of reduced accuracy, the evaluation of conductance histograms is too expensive to be a routine task. Highly accurate quantum transport computations are only computationally feasible for a few selected conformations and thus necessarily ignore the rich conformational space probed in experiments. To overcome these limitations, we investigate the potential of machine learning for modeling conductance histograms, in particular by Gaussian process regression. We show that by selecting specific structural parameters as features, Gaussian process regression can be used to efficiently predict the zero-bias conductance from molecular structures, reducing the computational cost of simulating conductance histograms by an order of magnitude. This enables the efficient calculation of conductance histograms even on the basis of computationally expensive first-principles approaches by effectively reducing the number of necessary charge transport calculations, paving the way toward their routine evaluation.

Anomalous (Exergonic) Behavior in the Transfer of Electrons between Donors and Acceptors: Mobility, Energy, Caloric Capacity, and Entropy

Understanding the kinetics of electron transfer reactions involves active research in physics, chemistry, biology, and nano-tech. Here, we propose a model to apply in a broader framework by establishing a connection between thermodynamics and kinetics. From a purely thermodynamic point of view, electronic transfer Marcus' theory is revisited; consequently, calculations of thermodynamic variables such as mobility, energy, and entropy are provided. More significantly, two different regimes are explicitly established. In the anomalous region, an exergonic process associated with negative heat capacity appears. Further, in the same region, mobility, energy, and entropy decrease when the temperature increases.

Sensing the quantized reactivity of graphene

We demonstrated that the variations measured in the quantum capacitance of single-layer graphene, envisioned here as a conceptual molecular model, depend on the chemical reactivity of the molecule and can be used as an analytical and sensing tool for environmental conditions. The variations are quantized as a function of the environmental changes and can be correlated with chemical reactivity indexes such as chemical hardness and softness. This not only constitutes a proof-of-principle that the chemical reactivity of graphene, as a single molecule, can be determined in situ by measuring the quantum capacitance, but also that these measurements can be used as an analytical tool.

Ab Initio QM/MM Simulation of Ferrocene Homogeneous Electron-Transfer Reaction

Here, we demonstrate the feasibility of hybrid computational methods to predict the homogeneous electron exchange between the ferrocene and its oxidized (ferrocenium) state. The free energy for ferrocene oxidation was determined from thermodynamic cycles and implicit solvation strategies within density functional theory (DFT) methods leading to no more than 15% of deviation (in the range of 0.1-0.2 eV) when compared to absolute redox free energies obtained experimentally. Reorganization energy, as defined according to the Marcus theory of electron-transfer rate, was obtained by sampling the vertical ionization/electron affinity energies using hybrid quantum/classical (QM/MM) Born-Oppenheimer molecular dynamics trajectories. Calculated reorganization energies show a subtle but noteworthy dependence with the nature and the localization of the compensating countercharge. We concluded that the adopted hybrid computational strategy, to simulate homogeneous redox reactions, was successfully demonstrated and it further permits applications in more complex systems (required in daily life applications), where the electron transfer occurs heterogeneously.

Label-free capacitive assaying of biomarkers for molecular diagnostics

The label-free analysis of biomarkers offers important advantages in developing point-of-care (PoC) biosensors. In contrast to label-based methodologies, such as ELISA, label-free analysis enables direct detection of targets without additional steps and labeled reagents. Nonetheless, label-free approaches require high sensitivity to detect the intrinsic features of a biomarker and low levels of nonspecific signals. Electrochemical capacitance, [Formula: see text], is a feature of electroactive nanoscale films that can be measured using electrochemical impedance spectroscopy. [Formula: see text] is promising as an electrochemical transducing signal for the development of high-sensitivity, reagentless and label-free molecular diagnostic assays. We used a proprietary ferrocene (Fc)-tagged peptide that is able to self-assemble onto gold electrodes (thicknesses <2 nm) to which any biological receptor can be coupled. When coupled with biological receptors (e.g., a monoclonal antibody), [Formula: see text] exhibited by the redox-tagged peptide changes as a function of the target concentration. We provide herein the steps for the qualitative and quantitative detection of dengue non-structural protein 1 (NS1) biomarker. Detection of NS1 can be used to diagnose dengue virus infection, which causes epidemics each year in tropical and subtropical regions of the world. Including the pre-treatment of the electrode surface, the analysis takes ~25 h. This time can be reduced to minutes if the electrode surface is fabricated separately, demonstrating that [Formula: see text] is promising for PoC applications. We hope this protocol will serve as a reference point for researchers and companies that intend to further develop capacitive devices for molecular diagnostic assays.

Energy, Work, Entropy, and Heat Balance in Marcus Molecular Junctions

We present a consistent theory of energy balance and conversion in a single-molecule junction with strong interactions between electrons on the molecular linker (dot) and phonons in the nuclear environment where the Marcus-type electron hopping processes predominate in the electron transport. It is shown that the environmental reorganization and relaxation that accompany electron hopping energy exchange between the electrodes and the nuclear (molecular and solvent) environment may bring a moderate local cooling of the latter in biased systems. The effect of a periodically driven dot level on the heat transport and power generated in the system is analyzed, and energy conservation is demonstrated both within and beyond the quasistatic regime. Finally, a simple model of atomic scale engine based on a Marcus single-molecule junction with a driven electron level is suggested and discussed.

Introducing mesoscopic charge transfer rates into molecular electronics

It has been demonstrated that the concept of mesoscopic rate is able to establish a bridge between electrochemical and molecular electronic concepts.

Serological point-of-care and label-free capacitive diagnosis of dengue virus infection

Dengue non-structural protein 1 (NS1 DENV) is considered a biomarker for dengue fever in an early stage. A sensitive and rapid assay for distinguishing positive from negative dengue infection samples is imperative for epidemic control and public health in tropical regions because it enables the development of instantaneous updatable databases and effective surveillance systems. Presently, we successfully report, for the first time, the use of the electrochemical capacitive method for the detection of NS1 DENV biomarker in human serum samples. By using a ferrocene-tagged peptide modified surface containing anti-NS1 as the receptor, it was possible to differentiate positive from negative samples with a p < 0.01 in a reagentless and label-free capacitive format. This capacitive assay had a cut-off of 1.36% (confidence interval of 99.99%); it therefore opens new avenues for developing miniature label-free electrochemical devices for infectious diseases.

Quantum capacitance as a reagentless molecular sensing element

The application of nanoscale capacitance as a transduction of molecular recognition relevant to molecular diagnostics is demonstrated. The energy-related signal relates directly to the electron occupation of quantized states present in readily fabricated molecular junctions such as those presented by redox switchable self-assembled molecular monolayers, reduced graphene oxide or redox-active graphene composite films, assembled on standard metallic or micro-fabricated electrodes. Sensor design is thus based on the response of a confined and resolved electronic density of states to target binding and the associated change in interfacial chemical potential. Demonstrated herein with a number of clinically important markers, this represents a new potent and ultrasensitive molecular detection enabling energy transducer principle capable of quantifying, in a single step and reagentless manner, markers within biological fluid.

Mapping the ionic fingerprints of molecular monolayers

Molecular dynamics simulations support a self-assembled monolayer specific energy barrier to solution-phase ions that once surmounted, the entrapped ions support a film embedded ionic capacitance and non-faradaic relaxation (mapping through electrochemical capacitance measurements). The associated capacitance can be assigned as a particular case of general electrochemical capacitance.

Mesoscopic behaviour of multi-layered graphene: the meaning of supercapacitance revisited

The double layer capacitive phenomena is just a particular case of a more general quantum mechanical approach, wherein the electrochemical capacitance is central hence governing the super-capacitance phenomenology in general.

Molecular conductance of double-stranded DNA evaluated by electrochemical capacitance spectroscopy

Conductance was measured in two different double stranded DNA (both with 20 bases), the more conducting poly(dG)-poly(dC) (ds-DNAc) and the less conducting poly(dA)-poly(dT) (ds-DNAi), by means of Electrochemical Capacitance Spectroscopy (ECS). The use of the ECS approach, exemplified herein with DNA nanowires, is equally a suitable and time-dependent advantageous alternative for conductance measurement of molecular systems, additionally allowing better understanding of the alignment existing between molecular scale conductance and electron transfer rate.

Density functional theory and an experimentally-designed energy functional of electron density

We demonstrate that capacitance spectroscopy experimentally allows access to the energy associated with the quantum mechanical ground state of many-electron systems.