Fatokhoma A. Camara, Hamidréza Ramézani, Nathalie Mathieu
et al.
The adsorption of large organic molecules such as ofloxacin onto disordered nanoporous carbons presents significant challenges due to the complex interplay of adsorbate–adsorbent charge interactions, dipole moments, and pH-dependent speciation.
Using 2D infrared spectroscopy, we observe significant structural changes of light-harvesting complex II (LHCII) protein upon acidification. Despite the altered protein structure, the light-harvesting capacity of LHCII was not affected.
Yixuan Feng, Xavier R. Advincula, Hongwei Fang
et al.
Montmorillonite, a ubiquitous clay mineral, plays a vital role in geochemical and environmental processes due to its chemically complex edge surfaces. However, the molecular-scale acid-base reactivity of these interfaces remains poorly understood due to the limitations of both experimental resolution and conventional simulations. Here, we employ machine learning potentials with first-principles accuracy to perform nanosecond-scale molecular dynamics simulations of montmorillonite nanoparticles across a range of pH. Our results reveal clear amphoteric behavior: edge sites undergo protonation in acidic environments and deprotonation in basic conditions. Even at neutral pH, spontaneous and directional proton transfer events are common, proceeding via both direct and solvent-mediated pathways. These findings demonstrate that montmorillonite edges are not static arrays of hydroxyl groups but dynamic, proton-conducting networks whose reactivity is modulated by local structure and solution conditions. This work offers a molecular-level framework for understanding proton transport and buffering in clay-water systems, with broad implications for catalysis, ion exchange, and environmental remediation.
Diffusiophoresis of charged particles in the presence of electrolytes has been extensively studied in the literature. However, in these setups, particles typically move in a single direction, either up or down the electrolyte gradient. Here, we theoretically investigate the conditions under which a particle can reverse its diffusiophoretic direction within the same setup, leading to the formation of a focusing band under steady-state concentration gradients. Using multi-ion diffusiophoresis calculations, we simulate particle transport in an acid-based reaction system where salt is added alongside the acid. For a range of salt concentrations, particles focus within the channel. Our analysis reveals that a pH-dependent zeta potential is necessary for this focusing to occur, and determines where the particles focus, i.e., on or off the acid-base reaction front. We report qualitative agreement with prior experimental observations and derive analytical conditions governing particle focusing, highlighting the delicate balance between concentration gradients and zeta potential variations. The work elucidates the crucial physics of pH-dependent zeta potential and opens new avenues for exploring diffusiophoresis in acid-base systems, with implications for microfluidic design and biophysical transport processes.
In this systematic study, ionic conductivity spectra of poly(diallyl-dimethylammonium)/poly(acrylic acid) (PDADMA/PAA)n polyelectrolyte multilayers (PEMs) are investigated regarding superposition principles.
Eliane Briand, Bartosz Kohnke, Carsten Kutzner
et al.
The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes. Conversely, conformational and environmental changes of the biomolecule affect the protonation state of these groups. With few exceptions, conventional force field-based molecular dynamics (MD) simulations do not account for these effects, nor do they allow for coupling to a pH buffer. Here we present a GROMACS implementation of a rigorous Hamiltonian interpolation $λ$-dynamics constant pH method, which rests on GPU-accelerated Fast Multipole Method (FMM) electrostatics. Our implementation supports both CHARMM36m and Amber99sb*-ILDN force fields and is largely automated to enable seamless switching from regular MD to constant pH MD, involving minimal changes to the input files. Here, the first of two companion papers describes the underlying constant pH protocol and sample applications to several prototypical benchmark systems such as cardiotoxin V, lysozyme, and staphylococcal nuclease. Enhanced convergence is achieved through a new dynamic barrier height optimization method, and high p$K_a$ accuracy is demonstrated. We use Functional Mode Analysis and Mutual Information to explore the complex intra- and intermolecular couplings between the protonation states of titratable groups as well as those between protonation states and conformational dynamics. We identify striking conformation-dependent p$K_a$ variations and unexpected inter-residue couplings. Conformation-protonation coupling is identified as a primary cause of the slow protonation convergence notorious to constant pH simulations involving multiple titratable groups, suggesting enhanced sampling methods to accelerate convergence.
M-N-C single-atom catalysts (SACs) have emerged as a potential substitute for the costly platinum-group catalysts in oxygen reduction reaction (ORR). However, several critical aspects of M-N-C SACs in ORR remain poorly understood, including their pH-dependent activity, selectivity for 2- or 4-electron transfer pathways, and the identification of the rate-determining steps. Herein, analyzing >100 M-N-C structures and >2000 sets of energetics, we unveil a pH-dependent evolution in ORR activity volcanos from a single-peak in alkaline media to a double-peak in acids. We found that this pH-dependent behavior in M-N-C catalysts fundamentally stems from their moderate dipole moments and polarizability for O* and HOO* adsorbates, as well as unique scaling relations among ORR adsorbates. To validate our theoretical discovery, we synthesized a series of molecular M-N-C catalysts, each characterized by well-defined atomic coordination environments. Impressively, the experiments matched our theoretical predictions on kinetic current, Tafel slope, and turnover frequency in both acidic and alkaline environments. These new insights also refine the famous Sabatier principle by emphasizing the need to avoid an "acid trap" while designing M-N-C catalysts for ORR or any other pH-dependent electrochemical applications.
Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties. Molecular simulations of nanoscopic atomistic structures therefore require accurately resolved three-dimensional input structures. If extracted from experiment, these structures often suffer from severe uncertainties, of which the lack of information on hydrogen atoms is a prominent example. Hence, experimental structures require careful review and curation, which is a time-consuming and error-prone process. Here, we present a fast and robust protocol for the automated structure analysis, and pH-consistent protonation, in short, ASAP. For biomolecules as a target, the ASAP protocol integrates sequence analysis and error assessment of a given input structure. ASAP allows for pKa prediction from reference data through Gaussian process regression including uncertainty estimation and connects to system-focused atomistic modeling described in (J. Chem. Theory Comput. 16, 2020, 1646). Although focused on biomolecules, ASAP can be extended to other nanoscopic objects, because most of its design elements rely on a general graph-based foundation guaranteeing transferability. The modular character of the underlying pipeline supports different degrees of automation, which allows for (i) efficient feedback loops for human-machine interaction with a low entrance barrier and for (ii) integration into autonomous procedures such as automated force field parametrizations. This facilitates fast switching of the pH-state through on-the-fly system-focused reparametrization during a molecular simulation at virtually no extra computational cost.
Maximilian Weingart, Siyu Chen, Clara Donat
et al.
Alkaline vents (AV) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, 3-dimensional chimney structures were formed under laboratory conditions, however, no in situ visualisation or testing of the gradients was possible. We develop a quasi-2-dimensional microfluidic model of alkaline vents that allows spatio-temporal visualisation of mineral precipitation in low volume experiments. Upon injection of an alkaline fluid into an acidic, iron-rich solution, we observe a diverse set of precipitation morphologies, mainly controlled by flow-rate and ion-concentration. Using microscope imaging and pH dependent dyes, we show that finger-like precipitates can facilitate formation and maintenance of microscale pH gradients and accumulation of dispersed particles in confined geometries. Our findings establish a model to investigate the potential of gradients across a semi-permeable boundary for early compartmentalisation, accumulation and chemical reactions at the origins of life.
Birk Fritsch, Andreas Körner, Thaïs Couasnon
et al.
Advanced in situ techniques based on electrons and X-rays are increasingly used to gain insights into fundamental materials dynamics in liquid media. Yet, ionizing radiation changes the solution chemistry. In this work, we show that ionizing radiation decouples the acidity from autoprotolysis. Consequently, pH is insufficient to capture the acidity of water-based systems under irradiation. Via radiolysis simulations, we provide a more conclusive description of the acid-base interplay. Finally, we demonstrate that acidity can be tailored by adjusting the dose rate and adding pH-irrelevant species. This opens up a huge parameter landscape for studies involving ionizing radiation.
Arthur V. Straube, Stefanie Winkelmann, Felix Höfling
This theoretical study concerns a pH oscillator based on the urea-urease reaction confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the phase flow and of the limit cycle, which controls the dynamics for giant vesicles and dominates the pronouncedly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, which are amenable to analytic treatments that are complemented by numerical solutions, and obtain the period and amplitude of the oscillations as well as the parameter domain, where oscillatory behavior persists. We show that the accuracy of these predictions is highly sensitive to the employed reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The faithful modeling of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms.
In this paper, we study electrostatic and structural properties between pH-responsive polyelectrolyte brushes by using a strong stretching theory accounting for excluded volume interactions, the density of polyelectrolyte chargeable sites and the Born energy difference between the inside and outside of the brush layer. In a free energy framework, we obtain self-consistent field equations to determine electrostatic properties between two pH-responsive polyelectrolyte brushes. We elucidate that in the region between two pH-responsive polyelectrolyte brushes, electrostatic potential at the centerline and osmotic pressure increase not only with excluded volume interaction, but also with density of chargeable sites on a polyelectrolyte molecule. Importantly, we clarify that when two pH-responsive polyelectrolyte brushes approach each other, the brush thickness becomes short and that a large excluded volume interaction and a large density of chargeable sites yield the enhanced contract of polyelectrolyte brushes. In addition, we also demonstrate how the influence of such quantities as pH, the number of Kuhn monomers, the density of charged sites, the lateral separation between adjacent polyelectrolyte brushes, Kuhn length on the electrostatic and structural properties between the two polyelectrolyte brushes is affected by the exclusion volume interaction. Finally, we investigate the influence of Born energy difference on the thickness of polyelectrolyte brushes and the osmotic pressure between two pH-responsive polyelectrolyte brushes.
Molecular-level insight into interfacial water at buried electrode interfaces is essential in elucidating many phenomena of electrochemistry, but spectroscopic probing of the buried interfaces remains challenging. Here, using surface-specific vibrational spectroscopy, we probe and identify the interfacial water orientation and interfacial electric field at the calcium fluoride (CaF2)-supported electrified graphene/water interface under applied potentials. Our data shows that the water orientation changes drastically at negative potentials (<-0.03 V vs. Pd/H2), from O-H group pointing down towards bulk solution to pointing up away from the bulk solution, which arises from charging/discharging not of the graphene but of the CaF2 substrate. The potential-dependent spectra are nearly identical to the pH-dependent spectra, evidencing that the applied potentials change the local pH (more than five pH units) near the graphene electrode even at a current density below 1 microamp per square centimeter. Our work provides molecular-level insights into the dissociation and reorganization of interfacial water on an electrode/electrolyte interface.
Sourav Maiti, Sunayana Mitra, Clinton A. Johnson
et al.
The dynamics of excess protons in the protic ionic liquid ethylammonium formate (EAF) have been investigated from femtosecond to microseconds using visible pump mid-infrared probe spectroscopy. The pH-jump following visible photoexcitation of a photoacid (8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt, HPTS) results in proton transfer to the formate of the EAF. The proton transfer predominantly occurs over picoseconds through a pre-formed hydrogen-bonded complex between HPTS and EAF. We investigate the longer range and longer timescale proton transport processes in the ionic liquid by obtaining the ground-state conjugate base (RO-) dynamics from the congested transient-infrared spectra. The spectral kinetics indicate that the protons diffuse only a few solvent shells from the parent photoacid before recombining with RO-. A kinetic isotope effect of near unity (kH/kD~1) suggests vehicular transfer and transport of excess protons in this ionic liquid. Our findings provide a comprehensive insight into the complete photoprotolytic cycle of excess protons in a protic ionic liquid.
We report a theoretical study of ion size effect on various properties in a soft nanochannel with pH-dependent charge density. We develop a free energy based mean-field theory taking into account ion size as well as pH-dependence of charged polyelectrolyte layer grafted on a rigid surface in an electrolyte. The influence of ion size on properties in a soft nanochannel is evaluated by numerically calculating ion number densities and electrostatic potential. We demonstrate that unlike in point-like ions, for finite sizes of ions, a uniform distribution of chargeable sites within the polyelectrolyte layer causes unphysical discontinuities in ion number densities not only for hydrogen ion but also for other kinds of ions. It is shown that the same cubic spatial distribution of chargeable sites as for point-like ions is necessary to ensure continuity of ion number density and zero ion transport at the polyelectrolyte layer - rigid solid interface. We find that considering finite ion size causes an increase in electrostatic potential and electroosmotic velocity and a decrease in ion number densities. More importantly, we demonstrate that in polyelectrolyte layer, pH-dependence of polyelectrolyte charge density makes accumulation of hydrogen ions stronger than for the other positive ion species in the electrolyte and such a tendency is further enhanced by considering finite ion size. In addition, we discuss how consideration of finite ion size affects the role of various parameters on electrostatic and electroosmotic properties.
Photoelectrochemical water splitting is a promising route to produce hydrogen from solar energy. However, corrosion of semiconducting photoelectrodes remains a fundamental challenge for their practical application. The stability of BiVO4, one of the best performing photoanode materials, is systematically examined here using an illuminated scanning flow cell to measure its dissolution operando. The dissolution rates of BiVO4 under illumination depend on the electrolyte and decrease in the order: borate (pH=9.3) > phosphate (pH=7.2) > citrate (pH=7.0). BiVO4 exhibits an inherent lack of stability during the oxygen evolution reaction (OER), while hole-scavenging citrate electrolyte offers kinetic protection. The dissolution of Bi peaks at different potentials than the dissolution of V in phosphate buffer, whereas both ions dissolve simultaneously in borate buffer. The life cycle of a 90 nm BiVO4 film is monitored during one hour of light-driven OER in borate buffer. The photocurrent and dissolution rates show independent trends with time, highlighting the importance to measure both quantities operando. Dissolution rates are correlated to the surface morphology and chemistry characterized using electron microscopy, X-ray photoelectron spectroscopy and atom probe tomography. These correlative measurements further the understanding on corrosion processes of photoelectrodes down to the nanoscopic scale to facilitate their future developments.
Protons at the water/vapor interface are relevant for atmospheric and environmental processes, yet to characterize their surface affinity on the quantitative level is still challenging. Here we utilize phase-sensitive sum-frequency vibrational spectroscopy to quantify the surface density of protons (or their hydronium form) at the intrinsic water/vapor interface, through inspecting the surface-field-induced alignment of water molecules in the electrical double layer of ions. With hydrogen halides in water, the surface adsorption of protons is found to be independent of specific proton-halide anion interactions and to follow a constant adsorption free energy, G about -3.74 (+/-0.56) kJ/mol, corresponding to a reduction of the surface pH with respect to the bulk value by 0.66 (+/-0.10), for bulk ion concentrations up to 0.3 M. Our spectroscopic study is not only of importance in atmospheric chemistry, but also offers a microscopic-level basis to develop advanced quantum-mechanical models for molecular simulations.
The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we show similarity between both methods {under certain conditions}. We perform molecular dynamics simulations of a weak polyelectrolyte in order to compare the titration curves obtained by both approaches. Our findings reveal a good agreement between the methods when the reaction ensemble is used to sweep the reaction constant. Pronounced differences between the reaction ensemble and the constant pH method can be observed for stronger acids and bases in terms of adaptive pH values. These deviations are due to the presence of explicit protons in the reaction ensemble method which induce a screening of electrostatic interactions between the charged titrable groups of the polyelectrolyte. The outcomes of our simulation hint to a better applicability of the reaction ensemble method for systems in confined geometries and titrable groups in polyelectrolytes with different pK$_\text{a}$ values.
The design of better heterogeneous catalysts for applications such as fuel cells and electrolyzers requires a mechanistic understanding of electrocatalytic reactions and the dependence of their activity on operating conditions such as pH. A satisfactory explanation for the unexpected pH dependence of electrochemical properties of platinum surfaces has so far remained elusive, with previous explanations resorting to complex co-adsorption of multiple species and resulting in limited predictive power. This knowledge gap suggests that the fundamental properties of these catalysts are not yet understood, limiting systematic improvement. Here, we analyze the change in charge and free energies upon adsorption using density-functional theory (DFT) to establish that water adsorbs on platinum step edges across a wide voltage range, including the double-layer region, with a loss of approximately 0.2 electrons upon adsorption. We show how this as-yet unreported change in net surface charge due to this water explains the anomalous pH variations of the hydrogen underpotential deposition (Hupd) and the potentials of zero total charge (PZTC) observed in published experimental data. This partial oxidation of water is not limited to platinum metal step edges, and we report the charge of the water on metal step edges of commonly used catalytic metals, including copper, silver, iridium, and palladium, illustrating that this partial oxidation of water broadly influences the reactivity of metal electrodes.