When do defectless alkanethiol SAMs in ionic liquids become penetrable? A molecular dynamics study

Molecular dynamics simulations were performed to address the permeability of defectless alkanethiol self-assembled monolayers (SAMs) on charged and uncharged Au(111) surfaces in 1-butyl-3-methylimidazolium ([bmim][BF4]) room-temperature ionic liquid (IL). We demonstrate that ionic permeation into the monolayer does not start until a critical surface charge density value is attained (both for positive and negative surface charges). The free energy barrier for the permeation of IL components is shown to include nearly equal contributions from ion desolvation and the channel formation in the dense monolayer. Long chain alkanethiols (hexadecanethiol SC16H33) exhibit superior barrier properties as compared with short chain alkanethiols (hexanethiol SC6H13) due to the dense packing of alkanethiol chains in highly ordered zigzag conformation oriented at the same tilt angle. Computed critical charge densities correspond to the electrode potential values beyond the limits of the monolayer stability, which might indicate the impermeability of the defectless monolayer towards the IL components. Experimental findings on increased interfacial capacitance are interpreted, therefore as some manifestation of the monolayer defectiveness occurring in real electrochemical systems. The potential of the mean force is constructed for a typical redox probe ferrocene/ferrocenium (Fc/Fc(+)) as well, to investigate a possible permeation of the solute from the IL into the SC6H13 monolayer.

Reactions of Superoxide with Iron Porphyrins in the Bulk and the Near-Surface Region of Ionic Liquids

The redox reaction of superoxide (KO2) with highly charged iron porphyrins (Fe(P4+), Fe(P8+), and Fe(P8-)) has been investigated in the ionic liquids (IL) [EMIM][Tf2N] (1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) and [EMIM][B(CN)4] (1-ethyl-3-methylimidazolium tetracyanoborate) by using time-resolved UV/vis stopped-flow, electrochemistry, cryospray mass spectrometry, EPR, and XPS measurements. Stable KO2 solutions in [EMIM][Tf2N] can be prepared up to a 15 mM concentration and are characterized by a signal in EPR spectrum at g = 2.0039 and by the 1215 cm(-1) stretching vibration in the resonance Raman spectrum. While the negatively charged iron porphyrin Fe(P8-) does not react with superoxide in IL, Fe(P4+) and Fe(P8+) do react in a two-step process (first a reduction of the Fe(III) to the Fe(II) form, followed by the binding of superoxide to Fe(II)). In the reaction with KO2, Fe(P4+) and Fe(P8+) show similar rate constants (e.g., in the case of Fe(P4+): k1 = 18.6 ± 0.5 M(-1) s(-1) for the first reaction step, and k2 = 2.8 ± 0.1 M(-1) s(-1) for the second reaction step). Notably, these rate constants are four to five orders of magnitude lower in [EMIM][Tf2N] than in conventional solvents such as DMSO. The influence of the ionic liquid is also apparent during electrochemical experiments, where the redox potentials for the corresponding Fe(III)/Fe(II) couples are much more negative in [EMIM][Tf2N] than in DMSO. This modified redox and kinetic behavior of the positively charged iron porphyrins results from their interactions with the anions of the ionic liquid, while the nucleophilicity of the superoxide is reduced by its interactions with the cations of the ionic liquid. A negligible vapor pressure of [EMIM][B(CN)4] and a sufficient enrichment of Fe(P8+) in a close proximity to the surface enabled XPS measurements as a case study for monitoring direct changes in the electronic structure of the metal centers during redox processes in solution and at liquid/solid interfaces.

Ionic liquid based approach for single-molecule electronics with cobalt contacts

An electrochemical method is presented for fabricating cobalt thin films for single-molecule electrical transport measurements. These films are electroplated in an aqueous electrolyte, but the crucial stages of electrochemical reduction to remove surface oxide and adsorption of alkane(di)thiol target molecules under electrochemical control to form self-assembled monolayers which protect the oxide-free cobalt surface are carried out in an ionic liquid. This approach yields monolayers on Co that are of comparable quality to those formed on Au by standard self-assembly protocols, as assessed by electrochemical methods and surface infrared spectroscopy. Using an adapted scanning tunneling microscopy (STM) method, we have determined the single-molecule conductance of cobalt/1,8-octanedithiol/cobalt junctions by employing a monolayer on cobalt and a cobalt STM tip in an ionic liquid environment and have compared the results with those of experiments using gold electrodes as a control. These cobalt substrates could therefore have future application in organic spintronic devices such as magnetic tunnel junctions.

Temperature-Driven Changeover in the Electron-Transfer Mechanism of a Thermophilic Plastocyanin

Electron-transfer kinetics of the thermophilic protein Plastocyanin from Phormidium laminosum adsorbed on 1,ω-alkanedithiol self-assembled monolayers (SAMs) deposited on gold have been investigated. The standard electron-transfer rate constant has been determined as a function of electrode-protein distance and solution viscosity over a broad temperature range (0-90 °C). For either thin or thick SAMs, the electron-transfer regime remains invariant with temperature, whereas for the 1,11-undecanethiol SAM of intermediate chain length, a kinetic regime changeover from a gated or friction-controlled mechanism at low temperature (0-30 °C) to a nonadiabatic mechanism above 40 °C is observed. To the best of our knowledge, this is the first time a thermal-induced transition between these two kinetic regimes is reported for a metalloprotein.

Long-range electron transfer with myoglobin immobilized at Au/mixed-SAM junctions: mechanistic impact of the strong protein confinement

Horse muscle myoglobin (Mb) was tightly immobilized at Au-deposited ~15-Å-thick mixed-type (1:1) alkanethiol SAMs, HS-(CH₂)₁₁-COOH/HS-(CH₂)₁₁-OH, and placed in contact with buffered H₂O or D₂O solutions. Fast-scan cyclic voltammetry (CV) and a Marcus-equation-based analysis were applied to determine unimolecular standard rate constants and reorganization free energies for electron transfer (ET), under variable-temperature (15-55 °C) and -pressure (0.01-150 MPa) conditions. The CV signal was surprisingly stable and reproducible even after multiple temperature and pressure cycles. The data analysis revealed the following values: standard rate constant, 33 s⁻¹ (25 °C, 0.01 MPa, H₂O); reorganization free energy, 0.5 ± 0.1 eV (throughout); activation enthalpy, 12 ± 3 kJ mol⁻¹; activation volume, -3.1 ± 0.2 cm³ mol⁻¹; and pH-dependent solvent kinetic isotope effect (k(H)⁰/k(D)⁰), 0.7-1.4. Furthermore, the values for the rate constant and reorganization free energy are very similar to those previously found for cytochrome c electrostatically immobilized at the monocomponent Au/HS-(CH₂)₁₁-COOH junction. In vivo, Mb apparently forms a natural electrostatic complex with cytochrome b₅ (cyt-b₅) through the "dynamic" (loose) docking pattern, allowing for a slow ET that is intrinsically coupled to the water's removal from the "defective" heme iron (altogether shaping the biological repair mechanism for Mb's "met" form). In contrary, our experiments rather mimic the case of a "simple" (tight) docking of the redesigned (mutant) Mb with cyt-b₅ (Nocek et al. J. Am. Chem. Soc. 2010, 132, 6165-6175). According to our analysis, in this configuration, Mb's distal pocket (linked to the "ligand channel") seems to be arrested within the restricted configuration, allowing the rate-determining reversible ET process to be coupled only to the inner-sphere reorganization (minimal elongation/shortening of an Fe-OH₂ bond) rather than the pronounced detachment (rebinding) of water and, hence, to be much faster.

Ionic liquids: structure and photochemical reactions

Ionic liquids are subjects of intense current interest within the physical chemistry community. A great deal of progress has been made in just the past five years toward identifying the factors that cause these salts to have low melting points and other useful properties. Supramolecular structure and organization have emerged as important and complicated topics that may be key to understanding how chemical reactions and other processes are affected by ionic liquids. New questions are posed, and an active debate is ongoing regarding the nature of nanoscale ordering in ionic liquids. The topic of reactivity in ionic liquids is still relatively unexplored; however, the results that have been obtained indicate that distributed kinetics and dynamical heterogeneity may sometimes, but not always, be influencing factors.

Understanding chemical reaction mechanisms in ionic liquids: successes and challenges

The focus of this article is an examination of chemical reaction mechanisms in ionic liquids. These mechanisms are compared with those pertaining to the same reactions carried out in conventional solvents. In cases where the mechanisms differ, attempts to provide an explanation in terms of the chemical and physicochemical properties of the reactants and of the components of the ionic liquids are described. A wide range of reactions from different branches of chemistry has been selected for this purpose. A sufficient background for student readers has been included. This tutorial review should also be of interest to kineticists, and to both new and experienced investigators in the ionic liquids field.

Fundamental signatures of short- and long-range electron transfer for the blue copper protein azurin at Au/SAM junctions

The blue copper protein from Pseudomonas aeruginosa, azurin, immobilized at gold electrodes through hydrophobic interaction with alkanethiol self-assembled monolayers (SAMs) of the general type [-S-(CH(2))(n)-CH(3)] (n = 4, 10, and 15) was employed to gain detailed insight into the physical mechanisms of short- and long-range biomolecular electron transfer (ET). Fast scan cyclic voltammetry and a Marcus equation analysis were used to determine unimolecular standard rate constants and reorganization free energies for variable n, temperature (2-55 degrees C), and pressure (5-150 MPa) conditions. A novel global fitting procedure was found to account for the reduced ET rate constant over almost five orders of magnitude (covering different n, temperature, and pressure) and revealed that electron exchange is a direct ET process and not conformationally gated. All the ET data, addressing SAMs with thickness variable over ca. 12 A, could be described by using a single reorganization energy (0.3 eV), however, the values for the enthalpies and volumes of activation were found to vary with n. These data and their comparison with theory show how to discriminate between the fundamental signatures of short- and long-range biomolecular ET that are theoretically anticipated for the adiabatic and nonadiabatic ET mechanisms, respectively.

Unusual mechanism for the short-range electron transfer within gold-alkanethiol-ionic-liquid films of subnanometer thickness

Exploiting nanoscopically tunable composite gold-alkanethiol-ionic-liquid/ferrocene self-assembled systems with tunable electron transfer distance, we discovered in the case of thinner alkanethiol films a thermally activated electron transfer pattern totally controlled by the viscosity-related slow relaxation mode(s) of the ionic liquid acting as the reactant's fluctuating environment. This pattern manifested through the activation enthalpy and volume parameters that are identical to those for viscous flow was explained in terms of the extreme adiabatic mechanism with a vanishing Marcus barrier (via the exponential Franck-Condon-like term approaching unity).