Role of substrate unbinding in Michaelis-Menten enzymatic reactions

The Michaelis-Menten equation provides a hundred-year-old prediction by which any increase in the rate of substrate unbinding will decrease the rate of enzymatic turnover. Surprisingly, this prediction was never tested experimentally nor was it scrutinized using modern theoretical tools. Here we show that unbinding may also speed up enzymatic turnover--turning a spotlight to the fact that its actual role in enzymatic catalysis remains to be determined experimentally. Analytically constructing the unbinding phase space, we identify four distinct categories of unbinding: inhibitory, excitatory, superexcitatory, and restorative. A transition in which the effect of unbinding changes from inhibitory to excitatory as substrate concentrations increase, and an overlooked tradeoff between the speed and efficiency of enzymatic reactions, are naturally unveiled as a result. The theory presented herein motivates, and allows the interpretation of, groundbreaking experiments in which existing single-molecule manipulation techniques will be adapted for the purpose of measuring enzymatic turnover under a controlled variation of unbinding rates. As we hereby show, these experiments will not only shed first light on the role of unbinding but will also allow one to determine the time distribution required for the completion of the catalytic step in isolation from the rest of the enzymatic turnover cycle.

Characterisation of Complex Electrode Processes using Simultaneous Impedance Spectroscopy and Electrochemical Nanogravimetric Measurements

The methodology and illustrative examples of application are presented for a technique that simultaneously combines electrochemical impedance spectroscopy (EIS) and nanogravimetric measurements; the latter are implemented using a so-called electrochemical quartz crystal nanobalance (EQCN). The combination of EIS and EQCN provides a powerful method for the characterisation of many complex processes at electrochemical interfaces. This method gives in one relatively simple experiment more detailed information than is available from conventional electrochemical techniques. The combined measurements can be performed either as a function of time, at a constant electrode potential, or under potentiodynamic conditions, as a function of the electrode potential. Herein, we show how this can be applied to enable more accurate investigation of processes that occur at boundaries between electrodes and electrolytes. The application examples range from eletrocatalysis, in which evaluation of a catalyst is performed simultaneously with its formation, and the intercalation and electrodeposition of thin metal films to in situ characterisation of non-electroactive self-assembled monolayers during their formation.

The simplest model of charge storage in single file metallic nanopores

The problem of voltage controlled accumulation of ions in a narrow nanopore, which can accommodate just one row of ions of an ionic liquid and is filled with ions when the electrode is unpolarised, is mapped on an exactly solvable one-dimensional two state lsing model. Analytical solution of this, presumably simplest, statistical mechanical model reveals the dependence of the electrical capacitance on voltage, pore radius, and temperature. The voltage dependence of capacitance has the character of a smeared resonance, whose position and height is affected by a tiny change of the pore radius. Consequently, even the slightest dispersion of pore radii in the whole electrode, unavoidable in any real system, softens the voltage dependence.

Extending the shell-isolated nanoparticle-enhanced Raman spectroscopy approach to interfacial ionic liquids at single crystal electrode surfaces

We employ, for the first time, SHINERS to study single crystal electrode surfaces in ionic liquids, and combine DFT calculations to elucidate the structural details of imidazolium-based ionic liquid–Au single crystal electrode interfaces.

On the dual character of charged metal–molecule hybrids and the opposite behaviour of the forward and reverse CT processes

Charged molecules bonded to metals show two kinds of electronic structures depending on the charge of the metal.

Tailoring the catalytic activity of electrodes with monolayer amounts of foreign metals

During the past decade, electrocatalysis has attracted significant attention primarily due to the increased interest in the development of new generations of devices for electrochemical energy conversion. This has resulted in a progress in both fundamental understanding of the complex electrocatalytic systems and in the development of efficient synthetic schemes to tailor the surface precisely at the atomic level. One of the viable concepts in electrocatalysis is to optimise the activity through the direct engineering of the properties of the topmost layers of the surface, where the reactions take place, with monolayer and sub-monolayer amounts of metals. This forms (bi)metallic systems where the electronic structure of the active sites is optimised using the interplay between the nature and position of the atoms of solute metals at the surface. In this review, we focus on recent theoretical and experimental achievements in designing efficient (bi)metallic electrocatalysts with selective positioning of foreign atoms to form a variety of active catalytic sites at the electrode surface. We summarize recent results published in the literature and outline challenges for computational and experimental electrocatalysis to engineer active and selective catalysts using atomic layers.

Localized electrochemical impedance spectroscopy: visualization of spatial distributions of the key parameters describing solid/liquid interfaces

Acquisition of localized electrochemical impedance spectra as a function of spatial coordinates combined with novel approaches of data analysis brings a key for visualization of two-dimensional distributions of important parameters describing solid/liquid interfaces. They include the capacitance of the electric double layer, the resistance of the interfacial charge transfer, capacitances of adsorption, or other parameters depending on the properties of the system. Additionally, the proposed approach eliminates many common methodological problems of localized electrochemical impedance microscopies related to the frequency dependence of the actual pictures and difficulties with raw data interpretation. Thus, it offers a unique insight into the localized processes at the interface which is not possible to achieve using classical techniques.

Adsorption of Solvent Cations on Au(111) and Au(100) in Alkylimidazolium-Based Ionic Liquids – Worm-Like versus Micelle-Like Structures

By employing high resolution in-situ STM, the adsorption of alkylimidazolium-based cations of EMI + , PMI + , BMI + and OMI + on Au(111) and Au(100) surfaces are investigated systematically. The cation adsorption on both Au(111) and Au(100) are composed of double rows arising from counter-facing imidazolium-based cation pairs. On Au(100), the double rows associated with the four cations show micelle-like appearance along the two √ 2 directions of the Au(100) surface lattice units. The width of the double rows varies depending on the side chain length of the cations, but is constrained by the periodicity along the √ 2 directions. Anions of BF 4 - , PF 6 - , CF3SO 3 - and Tf2N - do not influence the micelle-like adsorption structure. On Au(111), the double rows are formed only when the terraces are etched to several atoms wide. Most likely, the underneath Au surface experiences restructuring to accommodate the double row structure, and the worm-like orientation of the double rows is the consequence of strain release. Both the micelle-like and worm-like adsorption structures would be lifted upon cathodic potential excursions when the surfaces are driven to undergo ordinary Au(100)-hex and Au(111)-(√ 3 × 22) reconstructions. These results reveal that the ordered micelle-like structure on Au(100) and the irregular worm-like structure on Au(111) are of the same nature.

Electrochemical tunnelling sensors and their potential applications

The quantum-mechanical tunnelling effect allows charge transport across nanometre-scale gaps between conducting electrodes. Application of a voltage between these electrodes leads to a measurable tunnelling current, which is highly sensitive to the gap size, the voltage applied and the medium in the gap. Applied to liquid environments, this offers interesting prospects of using tunnelling currents as a sensitive tool to study fundamental interfacial processes, to probe chemical reactions at the single-molecule level and to analyse the composition of biopolymers such as DNA, RNA or proteins. This offers the possibility of a new class of sensor devices with unique capabilities.

Advances in supramolecularly assembled nanostructures of fullerenes and porphyrins at surfaces

The ‘bottom-up’ strategy is an attractive and promising approach for the construction of nanoarchitectures. Supramolecular assemblies based on non-covalent interactions have been explored in an attempt to control surface properties. In this minireview, we focus on advances made in the past three years in the field of scanning tunneling microscopy (STM) on supramolecular assembly and the function of porphyrins, phthalocyanines, and fullerenes, non-covalently bound on metal single crystal surfaces. Well-defined adlayers, consisting of porphyrin and phthalocyanine for the design of supramolecular nanoarchitectures, supramolecular traps of C 60 on hydrogen bond networks, a unique approach for controlling molecular orientation by a 1:1 supramolecularly assembled film consisting of C 60 and the related derivatives and metallooctaethylporphyrins, and nanoapplications of fullerenes, either induced by tip manipulation or driven by thermal fluctuations at surfaces, were clearly visualized by STM.

Interfacial electrochemical electron transfer in biology - towards the level of the single molecule

Physical electrochemistry has undergone a remarkable evolution over the last few decades, integrating advanced techniques and theory from solid state and surface physics. Single-crystal electrode surfaces have been a core notion, opening for scanning tunnelling microscopy directly in aqueous electrolyte (in situ STM). Interfacial electrochemistry of metalloproteins is presently going through a similar transition. Electrochemical surfaces with thiol-based promoter molecular monolayers (SAMs) as biomolecular electrochemical environments and the biomolecules themselves have been mapped with unprecedented resolution, opening a new area of single-molecule bioelectrochemistry. We consider first in situ STM of small redox molecules, followed by in situ STM of thiol-based SAMs as molecular views of bioelectrochemical environments. We then address electron transfer metalloproteins, and multi-centre metalloenzymes including applied single-biomolecular perspectives based on metalloprotein/metallic nanoparticle hybrids.

An in situ STM/AFM and impedance spectroscopy study of the extremely pure 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate/Au(111) interface: potential dependent solvation layers and the herringbone reconstruction

The structure and dynamics of the interfacial layers between the extremely pure air- and water-stable ionic liquid 1-butyl-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate and Au(111) has been investigated using in situ scanning tunneling microscopy, cyclic voltammetry, electrochemical impedance spectroscopy, and atomic force microscopy measurements. The in situ scanning tunnelling microscopy measurements reveal that the Au(111) surface undergoes a reconstruction, and at -1.2 V versus Pt quasi-reference the famous (22 × √3) herringbone superstructure is probed. Atomic force microscopy measurements show that multiple ion pair layers are present at the ionic liquid/Au interface which are dependent on the electrode potential. Upon applying cathodic electrode potentials, stronger ionic liquid near surface structure is detected: both the number of near surface layers and the force required to rupture these layers increases. The electrochemical impedance spectroscopy results reveal that three distinct processes take place at the interface. The fastest process is capacitive in its low-frequency limit and is identified with electrochemical double layer formation. The differential electrochemical double layer capacitance exhibits a local maximum at -0.2 V versus Pt quasi-reference, which is most likely caused by changes in the orientation of cations in the innermost layer. In the potential range between -0.84 V and -1.04 V, a second capacitive process is observed which is slower than electrochemical double layer formation. This process seems to be related to the herringbone reconstruction. In the frequency range below 1 Hz, the onset of an ultraslow faradaic process is found. This process becomes faster when the electrode potential is shifted to more negative potentials.

Electrochemical crystallization of plasmonic nanostructures

We show how gold recrystallizes when under the influence of electrochemical potentials. This "cold annealing" occurs without charge transfer reactions and preserves nanoscale structural features. By performing the process on plasmonic nanostructures, grain growth is monitored noninvasively by optical spectroscopy. In this way, the influence from crystal structure on plasmon resonances can be investigated independently. Observed spectral changes are in excellent agreement with analytical models and changes in electron relaxation time and plasma frequency are calculated.

The Pt(111)/electrolyte interface under oxygen reduction reaction conditions: an electrochemical impedance spectroscopy study

The Pt(111)/electrolyte interface has been characterized during the oxygen reduction reaction (ORR) in 0.1 M HClO(4) using electrochemical impedance spectroscopy. The surface was studied within the potential region where adsorption of OH* and O* species occur without significant place exchange between the adsorbate and Pt surface atoms (0.45-1.15 V vs RHE). An equivalent electric circuit is proposed to model the Pt(111)/electrolyte interface under ORR conditions within the selected potential window. This equivalent circuit reflects three processes with different time constants, which occur simultaneously during the ORR at Pt(111). Density functional theory (DFT) calculations were used to correlate and interpret the results of the measurements. The calculations indicate that the coadsorption of ClO(4)* and Cl* with OH* is unlikely. Our analysis suggests that the two-dimensional (2D) structures formed in O(2)-free solution are also formed under ORR conditions.

Electrochemically controlled self-assembled monolayers characterized with molecular and sub-molecular resolution

Self-assembled organization of functional molecules on solid surfaces has developed into a powerful and sophisticated tool for surface chemistry and nanotechnology. A number of reviews on the topic have been available since the mid 1990s. This perspective article aims to focus on recent development in the investigations of electronic structures and assembling dynamics of electrochemically controlled self-assembled monolayers (SAMs) of thiol containing molecules on gold surfaces. A brief introduction is first given and particularly illustrated by a Table summarizing the molecules studied, the surface lattice structures and the experimental operating conditions. This is followed by discussion of two major high-resolution experimental methods, scanning tunnelling microscopy (STM) and single-crystal electrochemistry. In Section 3, we briefly address choice of supporting electrolytes and substrate surfaces, and their effects on the SAM structures. Section 4 constitutes the major body of the article by offering some details of recent studies for the selected cases, including in situ monitoring of assembling dynamics, molecular electronic structures, and the key external factors determining the SAM packing. In Section 5, we give examples of what can be offered by theoretical computations for the detailed understanding of the SAM electronic structures revealed by STM images. A brief summary of the current applications of SAMs in wiring metalloproteins, design and fabrication of sensors, and single-molecule electronics is described in Section 6. In the final two sections (7 and 8), we discuss the current status in understanding of electronic structures and properties of SAMs in electrochemical environments and what could be expected for future perspectives.

Substrate-induced varied conformation and molecular assemblies: in situ STM observation of beta-substituted oligothiophene adlayers on Au(111)

The adsorption of 3,3'''-dihexyl-2,2':5',2'':5'',2'''-quaterthiophene (4T) molecules on an Au(111) electrode was examined by using in situ scanning tunneling microscopy in 0.10 M HClO(4), revealing internal molecular structures of the tetrathiophene backbones and the hexyl side chains. The 4T admolecules were packed in lamellae with their molecular axis aligned along the main axis of the Au(111) substrate and their hexyl side chains interdigitated to enhance intermolecular interaction. Dynamics of molecular organization incurred by the shifting of potential was also observed in this study. By examining and comparing the adsorption of 4T on HOPG and Au(111), we address the role of the substrate in understanding the arrangement of 4T admolecules.