Numerical Correction of In Situ AFM-SECM Measurements.

Mass-transport-limited catalysis and membrane transport can be characterized by concentration profiles surrounding active surfaces. Scanning electrochemical microscopy (SECM) is a tool that has been used to measure concentration profiles; however, the presence and geometry of the tip can distort these profiles due to hindered diffusion, which in turn alters chemical behavior at the catalytic surface. To fully characterize the behavior of surface features such as catalytic sites, it is essential to account for and analytically remove the effect of tip presence. In this work, atomic force microscopy-based SECM (AFM-SECM) measurements over poly(tetrafluoroethylene) (PTFE) and gold electrode surfaces are used to measure negative and positive-feedback approach curves, respectively. By inversely fitting these approach curves with a finite element method (FEM) model, we derive kinetic and geometric tip parameters that characterize the effect of tip presence. Tip effects may be removed in the model to estimate concentration profiles and reaction properties for the case where no tip is present. A maximum 120% increase in the concentration at one tip radii above the surface is observed due to the presence of the tip, where the concentration field is compressed vertically, in proportion to surface feature size and tip separation. Conical AFM-SECM tips, with a higher ratio of tip height to the base size, introduce less concentration distortion than disk-shaped AFM-SECM tips.

Infrequent metadynamics study of rare-event electrostatic channeling.

The efficiency of cascade reactions, which consist of multiple chemical transformations that occur in a single pot without purification steps, is limited by the transport efficiency of intermediates between adjacent steps. Electrostatic channeling is a proven strategy for intermediate transfer in natural chemical cascades, but implementation into artificial cascades remains a challenge. Here, we combine infrequent metadynamics (InMetaD), umbrella sampling (US), and kinetic Monte Carlo (KMC) models to computationally study the transfer mechanism of glucose-6-phosphate (G6P) on a poly-arginine peptide bridging hexokinase (HK) and glucose-6-dehydrogenase (G6PDH). Transport of G6P by hopping in the presence of poly-arginine peptides is shown to be a rare event, and InMetaD is used to compute the hopping activation energy. US simulations capture the configurational change in the desorption process and enable the determination of the desorption energy. Parameterized by these results, a KMC model is used to estimate transport efficiency for the bridged enzyme complex. Results are compared to a similar complex using a poly-lysine bridge, using kinetic lag time as a metric. Even at a high ionic strength of 120 mM, poly-arginine peptides may be capable of more efficient transport as compared to poly-lysine, with a predicted lag time of 6 seconds for poly-arginine, compared to a previously reported lag time of 59 seconds for poly-lysine. This work indicates that poly-arginine peptides may be an improved bridge structure for electrostatic channeling of anionic intermediates.

Integrated Experimental and Theoretical Studies on an Electrochemical Immunosensor.

Electrochemical immunosensors (EIs) integrate biorecognition molecules (e.g., antibodies) with redox enzymes (e.g., horseradish peroxidase) to combine the advantages of immunoassays (high sensitivity and selectivity) with those of electrochemical biosensors (quantitative electrical signal). However, the complex network of mass-transfer, catalysis, and electrochemical reaction steps that produce the electrical signal makes the design and optimization of EI systems challenging. This paper presents an integrated experimental and modeling framework to address this challenge. The framework includes (1) a mechanistic mathematical model that describes the rate of key mass-transfer and reaction steps; (2) a statistical-design-of-experiments study to optimize operating conditions and validate the mechanistic model; and (3) a novel dimensional analysis to assess the degree to which individual mass-transfer and reaction steps limit the EI's signal amplitude and sensitivity. The validated mechanistic model was able to predict the effect of four independent variables (working electrode overpotential, pH, and concentrations of catechol and hydrogen peroxide) on the EI's signal magnitude. The model was then used to calculate dimensionless groups, including Damkohler numbers, novel current-control coefficients, and sensitivity-control coefficients that indicated the extent to which the individual mass-transfer or reaction steps limited the EI's signal amplitude and sensitivity.

Markov-State Transition Path Analysis of Electrostatic Channeling.

Electrostatic channeling is a naturally occurring approach to control the flux of charged intermediates in catalytic cascades. Computational techniques have enabled quantitative understanding of such mechanisms, augmenting experimental approaches by modeling molecular interactions in atomic detail. In this work, we report the first utilization of a Markov-state model (MSM) to describe the surface diffusion of a reaction intermediate, glucose 6-phosphate, on an artificially modified cascade where hexokinase and glucose-6-phosphate dehydrogenase are covalently conjugated by a cationic oligopeptide bridge. Conformation space networks are used to represent intermediate transport on enzyme surfaces, along with committor probabilities that assess the desorption probability of the intermediate on each segment of the channeling pathway. For the region between the peptide bridge and downstream active site, the ionic strength dependence of desorption probability by MSM agreed well with that by transition state theory. A kinetic Monte Carlo model integrates parameters from different computational methods to evaluate the contribution of desorption during each step. The approach is validated by calculation of kinetic lag time, which agrees well with experimental results. These results further demonstrate the applicability of molecular simulations and advanced sampling techniques to the design of chemical networks.

Characterizing Electron Transport through Living Biofilms.

Here we demonstrate the method of electrochemical gating used to characterize electrical conductivity of electrode-grown microbial biofilms under physiologically relevant conditions.1 These measurements are performed on living biofilms in aqueous medium using source and drain electrodes patterned on a glass surface in a specialized configuration referred to as an interdigitated electrode (IDA) array. A biofilm is grown that extends across the gap connecting the source and drain. Potentials are applied to the electrodes (ES and ED) generating a source-drain current (ISD) through the biofilm between the electrodes. The dependency of electrical conductivity on gate potential (the average of the source and drain potentials, EG = [ED + ES]/2) is determined by systematically changing the gate potential and measuring the resulting source-drain current. The dependency of conductivity on gate potential provides mechanistic information about the extracellular electron transport process underlying the electrical conductivity of the specific biofilm under investigation. The electrochemical gating measurement method described here is based directly on that used by M. S. Wrighton2,3 and colleagues and R. W. Murray4,5,6 and colleagues in the 1980's to investigate thin film conductive polymers.

Simulation of intermediate transport in nanoscale scaffolds for multistep catalytic reactions.

Efficient catalytic cascades that involve several sequential reactions are found frequently in nature. The efficiency of multi-step biochemical pathways is enhanced by substrate channelling, wherein the product of one reaction is directed toward and acts as substrate to the next sequential reaction. Such mechanisms can partially overcome diffusion, which is often fast compared to reaction rates, and promotes loss of intermediates. Biochemical substrate channelling is achieved by the architecture and scaffolding of enzymes, and mimicking these natural structures could lead to innovative catalyst designs. We investigate the efficiency of two channelling approaches - electrostatic interactions and surface adsorption - through continuum modelling, to identify the limits of these modes and the extent to which they can interact. The model considers transport between two active sites where an intermediate is produced at the first active site and consumed at the second. The system includes mass transport through diffusion and migration, and reaction kinetics at the active sites. The effectiveness of this model is quantified by yield of the second reaction relative to the first. Channelling via proximity between active sites and via surface adsorption are found to be inefficient, requiring high values of the rate constant at the second active site to obtain significant yields. The introduction of electrostatic interactions, however, leads to yields of over 90% at much lower values of the rate constant.

Integration of Platinum Group Metal-Free Catalysts and Bilirubin Oxidase into a Hybrid Material for Oxygen Reduction: Interplay of Chemistry and Morphology.

Catalytic activity toward the oxygen reduction reaction (ORR) of platinum group metal-free (PGM-free) electrocatalysts integrated with an enzyme (bilirubin oxidase, BOx) in neutral media was studied. The effects of chemical and morphological characteristics of PGM-free materials on the enzyme enhancement of the overall ORR kinetics was investigated. The surface chemistry of the PGM-free catalyst was studied using X-ray Photoelectron Spectroscopy. Catalyst surface morphology was characterized using two independent methods: length-scale specific image analysis and nitrogen adsorption. Good agreement of macroscopic and microscopic morphological properties was found. Enhancement of ORR activity by the enzyme is influenced by chemistry and surface morphology of the catalyst itself. Catalysts with a higher nitrogen content, specifically pyridinic moieties, showed the greatest enhancement. Furthermore, catalysts with a higher fraction of surface roughness in the range of 3-5 nm exhibited greater performance enhancement than catalysts lacking features of this size.

Thermally activated long range electron transport in living biofilms.

Microbial biofilms grown utilizing electrodes as metabolic electron acceptors or donors are a new class of biomaterials with distinct electronic properties. Here we report that electron transport through living electrode-grown Geobacter sulfurreducens biofilms is a thermally activated process with incoherent redox conductivity. The temperature dependency of this process is consistent with electron-transfer reactions involving hemes of c-type cytochromes known to play important roles in G. sulfurreducens extracellular electron transport. While incoherent redox conductivity is ubiquitous in biological systems at molecular-length scales, it is unprecedented over distances it appears to occur through living G. sulfurreducens biofilms, which can exceed 100 microns in thickness.

Kinetics of redox polymer-mediated enzyme electrodes.

Oxygen-reducing enzyme electrodes are prepared from laccase of Trametes versicolor and a series of osmium-based redox polymer mediators covering a range of redox potentials from 0.11 to 0.85 V. Experimentally obtained current density generated by the film electrodes is analyzed using a one-dimensional numerical model to obtain kinetic parameters. The bimolecular rate constant for mediation is found to vary with mediator redox potential from 250 s(-1) M(-1) when mediator and enzyme are close in redox potential to 9.4 x 10(4) s(-1) M(-1) when the redox potential difference is large. The value of the bimolecular rate constant for the simultaneously occurring laccase-oxygen reaction is found to be 2.4 x 10(5) s(-1) M(-1). The relationship between mediator-enzyme overpotential and bimolecular rate constant is used to determine the optimum mediator redox potential for maximum power output of a hypothetical biofuel cell with a planar cathode and a reversible hydrogen anode. For laccase of T. versicolor (E(e)(0) = 0.82), the optimum mediator potential is 0.66 V (SHE), and a molecular structure is presented to achieve this result.