Water dynamics and sum-frequency generation spectra at electrode/aqueous electrolyte interfaces.

The dynamics of water at interfaces between an electrode and an electrolyte is essential for the transport of redox species and for the kinetics of charge transfer reactions next to the electrode. However, while the effects of electrode potential and ion concentration on the electric double layer structure have been extensively studied, a comparable understanding of dynamical aspects is missing. Interfacial water dynamics presents challenges since it is expected to result from the complex combination of water-water, water-electrode and water-ion interactions. Here we perform molecular dynamics simulations of aqueous NaCl solutions at the interface with graphene electrodes, and examine the impact of both ion concentration and electrode potential on interfacial water reorientational dynamics. We show that for all salt concentrations water dynamics exhibits strongly asymmetric behavior: it slows down at increasingly positively charged electrodes but it accelerates at increasingly negatively charged electrodes. At negative potentials water dynamics is determined mostly by the electrode potential value, but in contrast at positive potentials it is governed both by ion-water and electrode-water interactions. We show how these strikingly different behaviors are determined by the interfacial hydrogen-bond network structure and by the ions' surface affinity. Finally, we indicate how the structural rearrangements impacting water dynamics can be probed via vibrational sum-frequency generation spectroscopy.

Ultrafast Rotational and Translational Energy Relaxation in Neat Liquids.

The excess energy flow pathways during rotational and translational relaxation induced by rotational or translational excitation of a single molecule of and within each of four different neat liquids (H2O, MeOH, CCl4, and CH4) are studied using classical molecular dynamics simulations and energy flux analysis. For all four liquids, the relaxation processes for both types of excitation are ultrafast, but the energy flow is significantly faster for the polar, hydrogen-bonded (H-bonded) liquids H2O and MeOH. Whereas the majority of the initial excess energy is transferred into hindered rotations (librations) for rotational excitation in the H-bonded liquids, an almost equal efficiency for transfer to translational and rotational motions is observed in the nonpolar, non-H-bonded liquids CCl4 and CH4. For translational excitation, transfer to translational motions dominates for all liquids. In general, the energy flows are quite local; i.e., more than 70% of the energy flows directly to the first solvent shell molecules, reaching almost 100% for CCl4 and CH4. Finally, the determined validity of linear response theory for these nonequilibrium relaxation processes is quite solvent-dependent, with the deviation from linear response most marked for rotational excitation and for the nonpolar liquids.

Electron Flow Characterization of Charge Transfer for Carbonic Acid to Strong Base Proton Transfer in Aqueous Solution.

Protonation of the strong base methylamine CH3NH2 by carbonic acid H2CO3 in aqueous solution, HOCOOH···NH2CH3 → HOCOO-···+HNH2CH3, has been previously studied ( J. Phys. Chem. B 2016, 109, 2271-2280; J. Phys. Chem. B 2016, 109, 2281-2290) via Car-Parinnello molecular dynamics. This proton transfer (PT) reaction within a hydrogen (H)-bonded complex was found to be barrierless and very rapid, with key reaction coordinates comprising the proton coordinate, the H-bond separation RON, and a solvent coordinate, reflecting the water solvent rearrangement involved in the neutral to ion pair conversion. In the present work, the reaction's charge flow aspects are analyzed in detail, especially a description via Mulliken charge transfer for PT (MCTPT). A natural bond orbital analysis and some extensions of them are employed for the complex's electronic structure during the reaction trajectories. Results demonstrate that consistent with the MCTPT picture, the charge transfer (CT) occurs from a methylamine base nonbonding orbital to a carbonic acid antibonding orbital. A complementary MCTPT reaction product perspective of CT from the antibonding orbital of the HN+ moiety to the nonbonding orbital of the oxygen in the H-bond complex is also presented. σOH and σHN+ bond order expressions show this CT to occur within the H-bond OHN triad, an aspect key for simultaneous bond-breaking and -forming in the PT reaction.

A Model Electron Transfer Reaction in Confined Aqueous Solution.

Liquid water confined within nanometer-sized channels exhibits a strongly reduced local dielectric constant perpendicular to the wall, especially at the interface, and this has been suggested to induce faster electron transfer kinetics at the interface than in the bulk. We study a model electron transfer reaction in aqueous solution confined between graphene sheets with classical molecular dynamics. We show that the solvent reorganization energy is reduced at the interface compared to the bulk, which explains the larger rate constant. However, this facilitated solvent reorganization is due to the partial desolvation by the graphene sheet of the ions involved in the electron transfer and not to a local dielectric constant reduction effect.

Confined Water's Dielectric Constant Reduction Is Due to the Surrounding Low Dielectric Media and Not to Interfacial Molecular Ordering.

Liquid water confined within nanometer-sized channels exhibits a surprisingly low dielectric constant along the direction orthogonal to the channel walls. This is typically assumed to result from a pronounced heterogeneity across the sample: the dielectric constant would be bulk-like everywhere except at the interface, where it would be dramatically reduced by strong restrictions on interfacial molecules. Here we study the dielectric properties of water confined within graphene slit channels via classical molecular dynamics simulations. We show that the permittivity reduction is not due to any important alignment of interfacial water molecules, but instead to the long-ranged anisotropic dipole correlations combined with an excluded-volume effect of the low-dielectric confining material. The bulk permittivity is gradually recovered only over several nanometers due to the impact of long-range electrostatics, rather than structural features. This has important consequences for the control of, e.g., ion transport and chemical reactivity in nanoscopic channels and droplets.

Solvation Dynamics in Water. 4. On the Initial Regime of Solvation Relaxation.

It is shown, by means of numerical and analytic work, that initial molecular momenta play little significant role in the initial fast solvation relaxation that follows electronic excitation of, and charge creation for, a standard model system of a solute in water. Instead, the nonequilibrium dynamics are predominantly described by noninertial "steering" by the torques directly generated by the newly created charge distribution. It is this process that largely overcomes inertia and drives the relaxation dynamics on a time scale of a few tens of femtoseconds in the key initial regime of the dynamics. These results are discussed in the context of commonly employed descriptions such as inertial, Gaussian, and underdamped dynamical behavior.

Water dynamics at electrified graphene interfaces: a jump model perspective.

The reorientation dynamics of water at electrified graphene interfaces was recently shown [J. Phys. Chem. Lett., 2020, 11, 624-631] to exhibit a surprising and strongly asymmetric behavior: positive electrode potentials slow down interfacial water reorientation, while for increasingly negative potentials water dynamics first accelerates before reaching an extremum and then being retarded for larger potentials. Here we use classical molecular dynamics simulations to determine the molecular mechanisms governing water dynamics at electrified interfaces. We show that changes in water reorientation dynamics with electrode potential arise from the electrified interfaces' impacts on water hydrogen-bond jump exchanges, and can be quantitatively described by the extended jump model. Finally, our simulations indicate that no significant dynamical heterogeneity occurs within the water interfacial layer next to the weakly interacting graphene electrode.

Water Structure, Dynamics, and Sum-Frequency Generation Spectra at Electrified Graphene Interfaces.

The properties of water at an electrified graphene electrode are studied via classical molecular dynamics simulations with a constant potential approach. We show that the value of the applied electrode potential has dramatic effects on the structure and dynamics of interfacial water molecules. While a positive potential slows down the reorientational and translational dynamics of water, an increasing negative potential first accelerates the interfacial water dynamics before a deceleration at very large magnitude potential values. Further, our spectroscopic calculations indicate that the water rearrangements induced by electrified interfaces can be probed experimentally. In particular, the calculated water vibrational sum-frequency generation (SFG) spectra show that SFG specifically reports on the first two water layers at 0 V but that at larger magnitude applied potentials the resulting static field induces long-range contributions to the spectrum. Electrified graphene interfaces provide promising paradigm systems for comprehending both short- and long-range neighboring aqueous system impacts.

Extracellular Ca2+-Sensing Fluorescent Protein Biosensor Based on a Collagen-Binding Domain.

The importance of extracellular gradients of biomolecules is increasingly appreciated in the processes of tissue development and regeneration, in health and disease. In particular, the dynamics of extracellular calcium concentration is rarely studied. Here, we present a low affinity Ca2+ biosensor based on Twitch-2B fluorescent protein fused with the cellulose- and collagen-binding peptides. These recombinant chimeric proteins can bind cellulose and collagen scaffolds and enable scaffold-based biosensing of Ca2+ in the proximity of cells in live 3D tissue models. We found that the Twitch-2B mutant is compatible with intensity-based ratiometric and fluorescence lifetime imaging microscopy (FLIM) measurement formats, under one- and two-photon excitation modes. Furthermore, the donor fluorescence lifetime of the biosensor displays response to [Ca2+] over a range of ∼2-2.5 ns, making it attractive for multiplexed FLIM assays. To evaluate the performance of this biosensor in physiological measurements, we applied it to the live Lgr5-GFP mouse intestinal organoid culture and measured its responses to the changes in extracellular Ca2+ upon chelation with EGTA. When combined with spectrally resolved FLIM of lipid droplets using Nile red dye, we observed changes in cytoplasmic and basal membrane-associated lipid droplet composition in response to the extracellular Ca2+ depletion, suggesting that the intestinal epithelium can respond to and compensate such treatment. Altogether, our results demonstrate Twitch-2B as a prospective Ca2+ sensor for multiplexed FLIM analysis in a complex 3D tissue environment.

Dynamical Recrossing in the Intercalation Process of the Anticancer Agent Proflavine into DNA.

Intercalation into DNA is the interaction mode of some anthracycline antibiotics. Recently, the molecular mechanism of this process was explored using the static free energy landscape. Here we explore the dynamical effects in the intercalation of proflavine into DNA by calculating the transmission coefficient κ-providing a measure of the departure from transition state theory for the reaction rate constant-by examination of the recrossing events at the transition state. For that purpose, we first found the accurate transition state of this complex system-as judged by a committor analysis-using a set of all-atom simulations of total length 6.3 ms. In a subsequent calculation of the transmission coefficient κ in another extensive set of simulations the small value κ = 0.1 was found, indicating a significant departure from TST. Comparison of this result with Grote-Hynes and Kramers theories shows that neither theory is able to capture this complex system's recrossing events; the source of this striking failure is discussed, as are related aspects of the mechanism. This study suggests that, for biomolecular processes similar to this, dynamical effects essential for the process are complex in nature and require novel approaches for their elucidation.

Intact carbonic acid is a viable protonating agent for biological bases.

Carbonic acid H2CO3 (CA) is a key constituent of the universal CA/bicarbonate/CO2 buffer maintaining the pH of both blood and the oceans. Here we demonstrate the ability of intact CA to quantitatively protonate bases with biologically-relevant pKas and argue that CA has a previously unappreciated function as a major source of protons in blood plasma. We determine with high precision the temperature dependence of pKa(CA), pKa(T) = -373.604 + 16,500/T + 56.478 ln T. At physiological-like conditions pKa(CA) = 3.45 (I = 0.15 M, 37 °C), making CA stronger than lactic acid. We further demonstrate experimentally that CA decomposition to H2O and CO2 does not impair its ability to act as an ordinary carboxylic acid and to efficiently protonate physiological-like bases. The consequences of this conclusion are far reaching for human physiology and marine biology. While CA is somewhat less reactive than (H+)aq, it is more than 1 order of magnitude more abundant than (H+)aq in the blood plasma and in the oceans. In particular, CA is about 70× more abundant than (H+)aq in the blood plasma, where we argue that its overall protonation efficiency is 10 to 20× greater than that of (H+)aq, often considered to be the major protonating agent there. CA should thus function as a major source for fast in vivo acid-base reactivity in the blood plasma, possibly penetrating intact into membranes and significantly helping to compensate for (H+)aq's kinetic deficiency in sustaining the large proton fluxes that are vital for metabolic processes and rapid enzymatic reactions.

Benzimidazoles as Metal-Free and Recyclable Hydrides for CO2 Reduction to Formate.

We report a novel metal-free chemical reduction of CO2 by a recyclable benzimidazole-based organo-hydride, whose choice was guided by quantum chemical calculations. Notably, benzimidazole-based hydride donors rival the hydride-donating abilities of noble-metal-based hydrides such as [Ru(tpy)(bpy)H]+ and [Pt(depe)2H]+. Chemical CO2 reduction to the formate anion (HCOO-) was carried out in the absence of biological enzymes, a sacrificial Lewis acid, or a base to activate the substrate or reductant. 13CO2 experiments confirmed the formation of H13COO- by CO2 reduction with the formate product characterized by 1H NMR and 13C NMR spectroscopy and ESI-MS. The highest formate yield of 66% was obtained in the presence of potassium tetrafluoroborate under mild conditions. The likely role of exogenous salt additives in this reaction is to stabilize and shift the equilibrium toward the ionic products. After CO2 reduction, the benzimidazole-based hydride donor was quantitatively oxidized to its aromatic benzimidazolium cation, establishing its recyclability. In addition, we electrochemically reduced the benzimidazolium cation to its organo-hydride form in quantitative yield, demonstrating its potential for electrocatalytic CO2 reduction. These results serve as a proof of concept for the electrocatalytic reduction of CO2 by sustainable, recyclable, and metal-free organo-hydrides.

Renewable Hydride Donors for the Catalytic Reduction of CO2: A Thermodynamic and Kinetic Study.

Increasing atmospheric CO2 concentration and dwindling fossil fuel supply necessitate the search for efficient methods for CO2 conversion to fuels. Assorted studies have shown pyridine and its derivatives capable of (photo)electrochemically reducing CO2 to methanol, and some mechanistic interpretations have been proposed. Here, we analyze the thermodynamic and kinetic aspects of the efficacy of pyridines as hydride-donating catalytic reagents that transfer hydrides via their dihydropyridinic form. We investigate both the effects of functionalizing pyridinic derivatives with electron-donating and electron-withdrawing groups on hydride-transfer catalyst strength, assessed via their hydricity (thermodynamic ability) and nucleophilicity (kinetic ability), and catalyst recyclability, assessed via their reduction potential. We find that pyridines substituted with electron-donating groups have stronger hydride-donating ability (having lower hydricity and larger nucleophilicity values), but are less efficiently recycled (having more negative reduction potentials). In contrast, pyridines substituted with electron-withdrawing groups are more efficiently recycled, but are weaker hydride donors. Functional group modification favorably tunes hydride strength or efficiency, but not both. We attribute this problematic coupling between the strength and recyclability of pyridinic hydrides to their aromatic nature and suggest several avenues for overcoming this difficulty.

High-Throughput Analysis of Mitochondrial Oxygen Consumption.

Interest in the investigation of mitochondrial dysfunction has seen a resurgence over recent years due to the implication of such dysfunction in both drug-induced toxicity and a variety of disease states. Here we describe a methodology to assist in such investigations whereby the oxygen consumption of isolated mitochondria is assessed in a high-throughput fashion using a phosphorescent oxygen-sensitive probe , standard microtiter plates, and plate reader detection. The protocols provided describe the required isolation procedures, initial assay optimization, and subsequent compound screening. Typical data is also provided illustrating the expected activity levels as well as recommended plate maps and data analysis approaches.

Bringing in vitro analysis closer to in vivo: Studying doxorubicin toxicity and associated mechanisms in 3D human microtissues with PBPK-based dose modelling.

Doxorubicin (DOX) is a chemotherapeutic agent of which the medical use is limited due to cardiotoxicity. While acute cardiotoxicity is reversible, chronic cardiotoxicity is persistent or progressive, dose-dependent and irreversible. While DOX mechanisms of action are not fully understood yet, 3 toxicity processes are known to occur in vivo: cardiomyocyte dysfunction, mitochondrial dysfunction and cell death. We present an in vitro experimental design aimed at detecting DOX-induced cardiotoxicity by obtaining a global view of the induced molecular mechanisms through RNA-sequencing. To better reflect the in vivo situation, human 3D cardiac microtissues were exposed to physiologically-based pharmacokinetic (PBPK) relevant doses of DOX for 2 weeks. We analysed a therapeutic and a toxic dosing profile. Transcriptomics analysis revealed significant gene expression changes in pathways related to "striated muscle contraction" and "respiratory electron transport", thus suggesting mitochondrial dysfunction as an underlying mechanism for cardiotoxicity. Furthermore, expression changes in mitochondrial processes differed significantly between the doses. Therapeutic dose reflects processes resembling the phenotype of delayed chronic cardiotoxicity, while toxic doses resembled acute cardiotoxicity. Overall, these results demonstrate the capability of our innovative in vitro approach to detect the three known mechanisms of DOX leading to toxicity, thus suggesting its potential relevance for reflecting the patient situation. Our study also demonstrated the importance of applying physiologically relevant doses during toxicological research, since mechanisms of acute and chronic toxicity differ.

Predicting Hydride Donor Strength via Quantum Chemical Calculations of Hydride Transfer Activation Free Energy.

We propose a method to approximate the kinetic properties of hydride donor species by relating the nucleophilicity (N) of a hydride to the activation free energy ΔG⧧ of its corresponding hydride transfer reaction. N is a kinetic parameter related to the hydride transfer rate constant that quantifies a nucleophilic hydridic species' tendency to donate. Our method estimates N using quantum chemical calculations to compute ΔG⧧ for hydride transfers from hydride donors to CO2 in solution. A linear correlation for each class of hydrides is then established between experimentally determined N values and the computationally predicted ΔG⧧; this relationship can then be used to predict nucleophilicity for different hydride donors within each class. This approach is employed to determine N for four different classes of hydride donors: two organic (carbon-based and benzimidazole-based) and two inorganic (boron and silicon) hydride classes. We argue that silicon and boron hydrides are driven by the formation of the more stable Si-O or B-O bond. In contrast, the carbon-based hydrides considered herein are driven by the stability acquired upon rearomatization, a feature making these species of particular interest, because they both exhibit catalytic behavior and can be recycled.

Perspective: Structure and ultrafast dynamics of biomolecular hydration shells.

The structure and function of biomolecules can be strongly influenced by their hydration shells. A key challenge is thus to determine the extent to which these shells differ from bulk water, since the structural fluctuations and molecular excitations of hydrating water molecules within these shells can cover a broad range in both space and time. Recent progress in theory, molecular dynamics simulations, and ultrafast vibrational spectroscopy has led to new and detailed insight into the fluctuations of water structure, elementary water motions, and electric fields at hydrated biointerfaces. Here, we discuss some central aspects of these advances, focusing on elementary molecular mechanisms and processes of hydration on a femto- to picosecond time scale, with some special attention given to several issues subject to debate.

Nuclear Quantum Effects in Water Reorientation and Hydrogen-Bond Dynamics.

We combine classical and ring polymer molecular dynamics simulations with the molecular jump model to provide a molecular description of the nuclear quantum effects (NQEs) on water reorientation and hydrogen-bond dynamics in liquid H2O and D2O. We show that while the net NQE is negligible in D2O, it leads to a ∼13% acceleration in H2O dynamics compared to a classical description. Large angular jumps-exchanging hydrogen-bond partners-are the dominant reorientation pathway (just as in a classical description); the faster reorientation dynamics arise from the increased jump rate constant. NQEs do not change the jump amplitude distribution, and no significant tunneling is found. The faster jump dynamics are quantitatively related to decreased structuring of the OO radial distribution function when NQEs are included. This is explained, via a jump model analysis, by competition between the effects of water's librational and OH stretch mode zero-point energies on the hydrogen-bond strength.

Dihydropteridine/Pteridine as a 2H+/2e- Redox Mediator for the Reduction of CO2 to Methanol: A Computational Study.

Conflicting experimental results for the electrocatalytic reduction of CO2 to CH3OH on a glassy carbon electrode by the 6,7-dimethyl-4-hydroxy-2-mercaptopteridine have been recently reported [ J. Am. Chem. Soc. 2014 , 136 , 14007 - 14010 , J. Am. Chem. Soc. 2016 , 138 , 1017 - 1021 ]. In this connection, we have used computational chemistry to examine the issue of this molecule's ability to act as a hydride donor to reduce CO2. We first determined that the most thermodynamically stable tautomer of this aqueous compound is its oxothione form, termed here PTE. It is argued that this species electrochemically undergoes concerted 2H+/2e- transfers to first form the kinetic product 5,8-dihydropteridine, followed by acid-catalyzed tautomerization to the thermodynamically more stable 7,8-dihydropteridine PTEH2. While the overall conversion of CO2 to CH3OH by three successive hydride and proton transfers from this most stable tautomer is computed to be exergonic by 5.1 kcal/mol, we predict high activation free energies (ΔG‡HT) of 29.0 and 29.7 kcal/mol for the homogeneous reductions of CO2 and its intermediary formic acid product by PTE/PTEH2, respectively. These high barriers imply that PTE/PTEH2 is unable, by this mechanism, to homogeneously reduce CO2 on a time scale of hours at room temperature.