Light-driven post-translational installation of reactive protein side chains.

Post-translational modifications (PTMs) greatly expand the structures and functions of proteins in nature1,2. Although synthetic protein functionalization strategies allow mimicry of PTMs3,4, as well as formation of unnatural protein variants with diverse potential functions, including drug carrying5, tracking, imaging6 and partner crosslinking7, the range of functional groups that can be introduced remains limited. Here we describe the visible-light-driven installation of side chains at dehydroalanine residues in proteins through the formation of carbon-centred radicals that allow C-C bond formation in water. Control of the reaction redox allows site-selective modification with good conversions and reduced protein damage. In situ generation of boronic acid catechol ester derivatives generates RH2C• radicals that form the native (ß-CH2-γ-CH2) linkage of natural residues and PTMs, whereas in situ potentiation of pyridylsulfonyl derivatives by Fe(II) generates RF2C• radicals that form equivalent ß-CH2-γ-CF2 linkages bearing difluoromethylene labels. These reactions are chemically tolerant and incorporate a wide range of functionalities (more than 50 unique residues/side chains) into diverse protein scaffolds and sites. Initiation can be applied chemoselectively in the presence of sensitive groups in the radical precursors, enabling installation of previously incompatible side chains. The resulting protein function and reactivity are used to install radical precursors for homolytic on-protein radical generation; to study enzyme function with natural, unnatural and CF2-labelled post-translationally modified protein substrates via simultaneous sensing of both chemo- and stereoselectivity; and to create generalized 'alkylator proteins' with a spectrum of heterolytic covalent-bond-forming activity (that is, reacting diversely with small molecules at one extreme or selectively with protein targets through good mimicry at the other). Post-translational access to such reactions and chemical groups on proteins could be useful in both revealing and creating protein function.

Discovering Electrochemistry with an Electrochemistry-Informed Neural Network (ECINN).

Machine learning is increasingly integrated into chemistry research by guiding experimental procedures, correlating structure and function, interpreting large experimental datasets, to distill scientific insights that might be challenging with traditional methods. Such applications, however, largely focus on gaining insights via big data and/or big computation, while neglecting the valuable chemical prior knowledge dwelling in chemists' minds. In this paper, we introduce an Electrochemistry-Informed Neural Network (ECINN) by explicitly embedding electrochemistry priors including the Butler-Volmer (BV), Nernst and diffusion equations on the backbone of neural networks for multi-task discovery of electrochemistry parameters. We applied the ECINN to voltammetry experiments of F e 2 + / F e 3 + ${{\rm F}{{\rm e}}^{2+}/{\rm F}{{\rm e}}^{3+}}$ and R u N H 3 6 2 + / R u N H 3 6 3 + ${{\rm R}{\rm u}{\left({\rm N}{{\rm H}}_{3}\right)}_{6}^{2+{\rm \ }}/{\rm R}{\rm u}{\left({\rm N}{{\rm H}}_{3}\right)}_{6}^{3+{\rm \ }}}$ redox couples to discover electrode kinetics and mass transport parameters. Notably, ECINN seamlessly integrated mass transport with BV to analyze the entire voltammogram to infer transfer coefficients directly, so offering a new approach to Tafel analysis by outdating various mass transport correction methods. In addition, ECINN can help discover the nature of electron transfer and is shown to refute incorrect physics if imposed. This work encourages chemists to embed their domain knowledge into machine learning models to start a new paradigm of chemistry-informed machine learning for better accountability, interpretability, and generalization.

Rotating Disk Electrodes beyond the Levich Approximation: Physics-Informed Neural Networks Reveal and Quantify Edge Effects.

Physics-informed neural networks are used to characterize the mass transport to the rotating disk electrode (RDE), the most widely employed hydrodynamic electrode in electroanalysis. The PINN approach was first quantitatively verified via 1D simulations under the Levich approximation for cyclic voltammetry and chronoamperometry, allowing comparison of the results with finite difference simulations and analytical equations. However, the Levich approximation is only accurate for high Schmidt numbers (Sc > 1000). The PINN approach allowed consideration of smaller Sc, achieving an analytical level of accuracy (error <0.1%) comparable with independent numerical evaluation and confirming that the errors in the Levich equation can be as high as 3% when Sc = 1000 for rapidly diffusing species in aqueous solution. Entirely novel, the PINNs permit the solution of the 2D diffusion equation under cylindrical geometry incorporating radial diffusion and reveal the rotating disk electrode edge effect as a consequence of the nonuniform accessibility of the disc with greater currents flowing near the extremities. The contribution to the total current is quantified as a function of the rotation speed, disk radius, and analyte diffusion coefficient. The success in extending the theory for the rotating disk electrode beyond the Levich equation shows that PINNs can be an easier and more powerful substitute for conventional methods, both analytical and simulation based.

Reversible Cyclic Voltammetry and Non-Unity Stoichiometry: The Ag/AgBr/Br- Redox Couple.

The voltammetry of electrochemically reversible couples in which a soluble reactant is converted into an insoluble product is investigated computationally via simulation and, in the context of the Ag/AgBr/Br-redox couple, experimentally. The voltammetric waveshape is characterized and, when analyzed via apparent transfer coefficient analysis, shown to give rise to apparent transfer coefficients very considerably in excess of unity, leading to the generic insight for the characterization of electrode reactions involving solution and solid phase reactants.

Calcifying Coccolithophore: An Evolutionary Advantage Against Extracellular Oxidative Damage.

The evolutionary advantages afforded by phytoplankton calcification remain enigmatic. In this work, fluoroelectrochemical experiments reveal that the presence of a CaCO3 shell of a naturally calcifying coccolithophore, Coccolithus braarudii, offers protection against extracellular oxidants as measured by the time required for the switch-off in their chlorophyll signal, compared to the deshelled equivalents, suggesting the shift toward calcification offers some advantages for survival in the surface of radical-rich seawater.

Experimental Voltammetry Analyzed Using Artificial Intelligence: Thermodynamics and Kinetics of the Dissociation of Acetic Acid in Aqueous Solution.

Artificial intelligence (AI) is used to quantitatively analyze the voltammetry of the reduction of acetic acid in aqueous solution generating thermodynamic and kinetic data. Specifically, the variation of the steady-state current for the reduction of protons at a platinum microelectrode as a function of the bulk concentration of acetic acid is recorded and analyzed giving data in close agreement with independent measurements, provided the AI is trained with accurate and precise knowledge of diffusion coefficients of acetic acid, acetate ions, and H+.

Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter.

Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is near-universally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores─single cells encrusted with biogenic calcite─to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a single-species coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell.

Calcium Carbonate Dissolution from the Laboratory to the Ocean: Kinetics and Mechanism.

The ultimate fate, over the course of millennia, of nearly all of the carbon dioxide formed by humankind is for it to react with calcium carbonate in the world's oceans. Although, this reaction is of global relevance, aspects of the calcite dissolution reaction remain poorly described with apparent contradictions present throughout the expansive literature. In this perspective we aim to evidence how a lack of appreciation of the role of mass-transport may have hampered developments in this area. These insights have important implications for both idealised experiments performed under laboratory conditions and for the measurement and modelling of oceanic calcite sediment dissolution.

The application of physics-informed neural networks to hydrodynamic voltammetry.

Electrochemical problems are widely studied in flowing systems since the latter offer improved sensitivity notably for electro-analysis and the possibility of steady-state measurements for fundamental studies even with macro-electrodes. We report the exploratory use of Physics-Informed Neural Networks (PINNs) as potentially simpler, and easier way to implement alternatives to finite difference or finite element simulations to predict the effect of flow and electrode geometry on the currents observed in channel electrodes where the flow is constrained to a rectangular duct with the electrode embedded flush with the wall of the cell. Several problems are addressed including the evaluation of the transport limited current at a micro channel electrode, the transport of material between two adjacent electrodes in a channel flow and the response of an electrode where the electrode reaction follows a preceding chemical reaction. The approach is shown to give quantitative agreement in the limits for which existing solutions are known whilst offering predictions for the case of the previously unexplored CE reaction at a micro channel electrode.

Electrode kinetics from a single experiment: multi-amplitude analysis in square-wave chronoamperometry.

The recently introduced technique of square-wave chronoamperometry (SWCA) is studied under conditions of progressively increasing height of potential pulses (square-wave amplitude) within a single experiment. In multi-amplitude square-wave chronoamperometry (MA-SWCA) a potential modulation consisting of square-wave forward and reverse potential pulses is imposed on a constant mid-potential; the amplitude of pulses increases progressively during the experiment. This allows the fast and reliable estimation of kinetic parameters at a constant pulse frequency in a single experiment, based on the resulting feature known as the amplitude-based quasireversible maximum. The proposed methodology is tested by simulating the responses of a simple quasireversible electrode reaction of a dissolved redox couple and a surface confined electrode reaction. Compared with conventional square-wave voltammetry (SWV) and SWCA, MA-SWCA shows advantages in estimation of the standard rate constant in terms of simplicity, speed and efficiency for both studied electrode mechanisms.

Use of Artificial Intelligence in Electrode Reaction Mechanism Studies: Predicting Voltammograms and Analyzing the Dissociative CE Reaction at a Hemispherical Electrode.

Artificial intelligence (AI) is used to learn the key voltammetric characteristics of the dissociative CE mechanism via training from multiple simulations using bespoke code. This allows first for the prediction of voltammograms without the need for further simulations, given knowledge of the relevant experimental parameters (rate and equilibrium constants, electrode geometry, and diffusion coefficients). Second, it is applied to analyze noisy experimental voltammetry to characterize the mechanistic type and to successfully extract the key kinetic and thermodynamic parameters.

A bespoke reagent free amperometric chloride sensor for drinking water.

Chloride quantification is important in drinking water quality control. A bespoke, rapid and reagent free electrochemical method is reported for a simple and accurate chloride sensor specifically for mineral water without the need for added electrolyte. The voltammetry used embraces first the reduction of oxygen to clean and activate the electrode surface and ensure reproducibility without the requirement for any mechanical polishing, followed by silver chloride formation and stripping. A linear correlation was found with silver chloride stripping peak currents and chloride concentrations within the range of 0.4 mM to 3.2 mM on a silver macro disc electrode. The chloride concentrations in two different mineral water samples were measured giving excellent agreement with independent analysis.

Opto-Electrochemical Dissolution Reveals Coccolith Calcium Carbonate Content.

Coccoliths are plates of biogenic calcium carbonate secreted by calcifying marine phytoplankton; annually these phytoplankton are responsible for exporting >1 billion tonnes (1015  g) of calcite to the deep ocean. Rapid and reliable methods for assessing the degree of calcification are technically challenging because the coccoliths are micron sized and contain picograms (pg) of calcite. Here we pioneer an opto-eletrochemical acid titration of individual coccoliths which allows 3D reconstruction of each individual coccolith via in situ optical imaging enabling direct inference of the coccolith mass. Coccolith mass ranging from 2 to 400 pg are reported herein, evidencing both inter- and intra-species variation over four different species. We foresee this scientific breakthrough, which is independent of knowledge regarding the species and calibration-free, will allow continuous monitoring and reporting of the degree of coccolith calcification in the changing marine environment.

Visualising electrochemical reaction layers: mediated vs. direct oxidation.

Electrochemical treatments are widely used for 'clean up' in which toxic metals and organic compounds are removed using direct or mediated electrolysis. Herein we report novel studies offering proof of concept that spectrofluorometric electrochemistry can provide important mechanistic detail into these processes. A thin layer opto-electrochemical cell, with a carbon fibre (radius 3.5 µm) working electrode, is used to visualise the optical responses of the oxidative destruction of a fluorophore either directly, on an electrode, or via the indirect reaction of the analyte with an electrochemically formed species which 'mediates' the destruction. The optical responses of these two reaction mechanisms are first predicted by numerical simulation followed by experimental validation of each using two fluorescent probes, a redox inactive (in the electrochemical window) 1,3,6,8-pyrenetetrasulfonic acid and the redox-active derivative 8-hydroxypyrene-1,3,6-trisulfonic acid. In the vicinity of a carbon electrode held at different oxidative potentials, the contrast between indirect electro-destruction, chlorination, and direct oxidation is very obvious. Excellent agreement is seen between the numerically predicted fluorescence intensity profiles and experiment.

Dopamine oxidation at gold electrodes: mechanism and kinetics near neutral pH.

The two-electron electrochemical oxidation of dopamine is studied voltammetrically at gold macroelectrodes around neutral pH with simulations used to give kinetic and mechanistic data. In particular, the system shows "potential inversion" in which the thermodynamic oxidation potential of dopamine to form the corresponding semi-quinone formation occurs at a more positive potential than that of the oxidation of the semi-quinone to the quinone form. The use of Tafel slopes measured from the voltammograms as a function of the voltage scan rate is show to be a particularly sensitive indicator of mechanism showing the effect of the follow-up chemistry in which the two-electron oxidation product undergoes an irreversible cyclization reaction.

Fast electrodeposition of zinc onto single zinc nanoparticles.

The zinc deposition reaction onto metallic zinc has been investigated at the single particle level through the electrode-particle collision method in neutral solutions, and in respect of its dependence on the applied potential and the ionic strength of a sulphate-containing solution. Depending on the concentration of sulphate ions in solution, different amounts of metallic zinc were deposited on the single Zn nanoparticles. Specifically, insights into the electron transfer kinetics at the single particles were obtained, indicating an electrically early reactant-like transition state, which is consistent with the rate-determining partial de-hydration/de-complexation process. Such information on the reaction kinetics at the nanoscale is of vital importance for the development of more efficient and long-lasting nanostructured Zn-based negative electrodes for Zn-ion battery applications.

Guidelines for the Voltammetric Study of Electrode Reactions with Coupled Chemical Kinetics at an Arbitrary Electrode Geometry.

A powerful, unified, and simplifying mathematical approach for the theoretical treatment of first-order chemical kinetics coupled to interfacial charge transfers at electrodes of arbitrary geometry and size, both uniformly accessible and nonuniformly accessible to the electroactive species, is presented. The general CEC mechanism at spherical and disc electrodes is considered to test the validity and benefits of such an approach, based on the application of the so-called kinetic steady state, that enables the reduction of the multivariable problem of kinetic-diffusive differential equations to a single variable problem of a diffusion-only differential equation. This is solved both analytically and numerically, showing how this approach leads to general, simple, and efficient solutions for the study of the influence of coupled chemical kinetics on the voltammetric response. The voltammetry of the CEC mechanism is analyzed as a function of the kinetics and thermodynamics of the preceding and subsequent chemical reactions and of the electrode size (from macroelectrodes to ultramicroelectrodes) and shape (spherical and disc). Comparison with the responses of the CE, EC, and E mechanisms is included, proposing diagnosis criteria and procedures for quantitative analysis of experimental data.

Versatile Electrochemical Sensing Platform for Bacteria.

Bacterial infections present one of the leading causes of mortality worldwide, resulting in an urgent need for sensitive, selective, cost-efficient, and easy-to-handle technologies to rapidly detect contaminations and infections with pathogens. The presented research reports a fully functional chemical-detection principle, addressing all of the above-mentioned requirements for a successful biosensing device. With the examples of Escherichia coli and Neisseria gonorrheae, we present an electrochemical biosensor based on the bacterial expression of cytochrome c oxidase for the selective detection of clinically relevant concentrations within seconds after pathogen immobilization. The generality of the biochemical reaction, as well as the easy substitution of target-specific antibodies make this concept applicable to a large number of different pathogenic bacteria. The successful transfer of this semidirect detection principle onto inexpensive, screen-printed electrodes for portable devices represents a potential major advance in the field of biosensor development.

Optimising amperometric pH sensing in blood samples: an iridium oxide electrode for blood pH sensing.

Amperometric pH sensing in blood samples has been studied using iridium oxide electrodes. The iridium oxide electrodes are made by electrodeposition of iridium oxide onto an iridium micro-disc electrode from an alkaline solution of iridium(iii) oxide. The response of the electrode is studied in aqueous solutions and authentic samples of sheep's blood employing both cyclic voltammetry and square wave voltammetry. Uncertainties of pH measurement in blood samples via cyclic voltammetry (±0.07 pH units) were improved by a factor of two using square wave voltammetry (±0.03 pH units). Limitations of amperometric pH sensing in blood samples are considered as caused by the uncertainty of the required reference measurements (via a conventional glass electrode) and also the use of matrix-free and low ionic strength buffers to calibrate a standard glass electrode for the measurement of blood pH.

Electrochemical characterisation and comparison of transport in Nafion films and particles.

The diffusional transport of the dication and monocation of methyl viologen, MV2+ and MV+, in hydrated Nafion films and particles is studied electrochemically. Methodology is established for characterising the relative rates of transport and for evaluating the diffusion coefficient of the two ions. The transport in the particles is shown to be significantly faster than in films of similar thickness whilst the diffusion of MV2+ is confirmed to be faster than that of MV+.