Onset potential of cathodic corrosion of Pt is independent of the bulk electrolyte pH, while the degree of material dissolution is dictated by the interfacial cation concentration.
Cheng Zhu, Krishan Kanhaiya, Samir Darouich
et al.
Alumina and aluminum oxyhydroxides underpin chemical-engineering technologies from heterogeneous catalysis, corrosion protection, functional coatings, energy-storage devices, to biomedical components. Yet molecular models that predictively connect phase structure, pH-dependent surface chemistry, electrolyte organization, and adsorption across operating conditions remain limited. Here we introduce a unified INTERFACE Force Field (IFF) parameterization together with a curated, ready-to-use pH-resolved surface model database that provides the most accurate and transferable atomistic description of major alumina phases to date. The framework covers a-Al2O3, g-Al2O3, boehmite, diaspore, and gibbsite using a single, physically interpretable parameter set that is directly compatible with CHARMM, AMBER, OPLS-AA, CVFF, and PCFF. Across structural, thermodynamic, mechanical, and interfacial benchmarks, simulations reproduce experimental reference data with more than 95 percent accuracy, exceeding existing force fields and the reliability of current density-functional approaches. A key advance is the first transferable treatment of surface ionization and charge regulation across alumina phases over a broad range of pH values, enabling simulations of realistic solid electrolyte interfaces without phase-specific reparameterization. Quantitative reliability is demonstrated by reproducing trends in zeta potentials and pH-dependent adsorption of a corrosion inhibitor at alumina-water interfaces. Predicted adsorption free energies and surface contact times correlate with experiments across more than an order of magnitude. Relative to ML-DFT workflows, the speed 100 to 1000 times faster, reaching system sizes and time scales inaccessible to quantum methods. The results establish a predictive computational platform to design alumina-containing functional materials under realistic process conditions.
This work introduces a generic pH-sensitive polymer model that captures charge-conformation coupling, enabling mechanistic insights into pH-modulated hydrophobic collapse.
Julien Dupré de Baubigny, Corentin Tregouet, Elena N. Govorun
et al.
Self-assembly of polymers at liquid interfaces using non-covalent interactions has emerged as a promising technique to reversibly produce self-healing membranes. Besides the assembly process, it is also crucial to control the mechanical properties of these membranes. Here, we measure the interfacial rheological properties of PMAA-PPO (polymethacrylic acid - polypropylene oxide) polymer membranes assembled using hydrogen bonds at the interface between water and a polar oil, Mygliol. Varying the pH enables us to modify the degree of ionization of the PMAA chains, and hence their ability to establish hydrogen interactions with PPO. Frequency sweeps of the interfacial layers show a crossover between a viscous regime at low frequencies and an elastic regime at high frequencies. The crossover elastic modulus, measured one hour after the two phases were put into contact, decreases by a half over the pH range investigated, which can be accounted for by a decrease of the layer thickness as pH increases. Furthermore, we find that the crossover frequency varies exponentially with the degree of ionization of PMAA. To account for these observations, we propose a simple picture where the short PPO chains behave as non-covalent cross-linkers that bridge several PMAA chains. The dissociation rate and hence the crossover frequency are controlled by the number of PO units per PPO chain involved in the hydrogen bonds.
Arthur V. Straube, Guillermo Olicón Méndez, Stefanie Winkelmann
et al.
We study a two-variable dynamical system modeling pH oscillations in the urea-urease reaction within giant lipid vesicles -- a problem that intrinsically contains multiple, well-separated timescales. Building on an existing, deterministic formulation via ordinary differential equations, we resolve different orders of magnitude within a small parameter and analyze the system's limit cycle behavior using geometric singular perturbation theory (GSPT). By introducing two different coordinate scalings -- each valid in a distinct region of the phase space -- we resolve the local dynamics near critical fold points, using the extension of GSPT through such singular points due to Krupa and Szmolyan. This framework enables a geometric decomposition of the periodic orbits into slow and fast segments and yields closed-form estimates for the period of oscillation. In particular, we link the existence of such oscillations to an underlying biochemical asymmetry, namely, the differential transport across the vesicle membrane.
Quasi-forbidden electronic transitions in atoms and quasi-degenerate vibronic transitions in molecules serve as powerful probes of hypothetical temporal variations of fundamental constants. Computation of the sensitivity of a transition to a variation of the fine-structure constant is conventionally performed by numerical variation of the speed of light in sophisticated electronic structure calculations, and therewith several individual calculations have to be performed. An approach is presented herein that obtains sensitivity coefficients as first order perturbation to the Dirac-Coulomb Hamiltonian and allows their computation as expectation values of the relativistic kinetic energy and rest-mass operators. These are available in essentially all \emph{ab initio} relativistic electronic structure codes. Additionally, the corresponding operators for two-component Hamiltonians are derived, explicitly for the zeroth order regular approximation Hamiltonian. The approach is applied to demonstrate great sensitivity of highly charged polar molecules that were recently proposed for high-precision spectroscopy in [Zülch \emph{et al.}, arXiv:2203.10333[physics.chem-ph]]. In particular, a high sensitivity of a wealth of quasi-degenerate vibronic transitions in PaF$^{3+}$ and CeF$^{2+}$ to temporal variations of the fine-structure constant and the electron-proton mass ratio is shown.
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.
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base pairs that require protonation events to stabilize or perturb these interactions. Constant pH molecular dynamics (CpHMD) methods provide a reliable framework to explore the conformational and protonation space of dynamic structures and for robust calculations of pH-dependent properties, such as the pK$_\mathrm{a}$ of titrable sites. Despite growing biological evidence concerning pH regulation of certain motifs and in biotechnological applications, pH-sensitive in silico methods have rarely been applied to nucleic acids. In this work, we extended the stochastic titration CpHMD method to include RNA parameters from the standard $χ$OL3 AMBER force field and highlighted its capability to depict titration events of nucleotides in single-stranded RNAs. We validated the method using trimers and pentamers with a single central titrable site while integrating a well-tempered metadynamics approach into the st-CpHMD methodology (CpH-MetaD) using PLUMED. This approach enhanced the convergence of the conformational landscape and enabled more efficient sampling of protonation-conformation coupling. Our pK$_\mathrm{a}$ estimates agree with experimental data, validating the method's ability to reproduce electrostatic changes around a titrable nucleobase in single-stranded RNA. These findings provided molecular insight into intramolecular phenomena, such as nucleobase stacking and phosphate interactions, that dictate the experimentally observed pK$_\mathrm{a}$ shifts between different strands. Overall, this work validates both the st-CpHMD and the metadynamics integration as reliable tools for studying biologically relevant RNA systems.
Although Gillespie's algorithm is justified under a set of axioms based on the assumption of homogeneity of the system, many chemical systems deviate from this assumption, as is the case for reactions taking place in low-mobility media. Using instead the generalized q formalism, we propose a new stochastic simulation algorithm by redefining the probability with which a mu reaction occurs between t + tao and t + tao + delta tao as P(tao q, mu) = a mu exp q(-a0 tao q), taking into account the separation of the natural exponential by the q parameter. Our algorithm has been implemented in the study of binary annihilation reactions, demonstrating a wider amplitude within the range of established physicochemical reactions, being the stochastic Gillespie scheme and the classical deterministic approach, particular cases of this new proposal. The effect of the nonextensivity parameter, q, on the reaction rate is analyzed and its relationship with the reaction order, n, and the heterogeneity parameter, h, is determined for two different reactant concentrations in the annihilation reaction. Different behaviors of these parameters are observed for the two types of samples, especially as q moves away from 1, confirming that quasi-second order reactions occur when reactant concentrations are similar and quasi-first order reactions when they are different. Empirical expressions between the classical reaction order and the degree of heterogeneity are proposed. The results obtained allow us to associate the behavior of sub and supra Arrhenius kinetics reported in other different reactions with the degree of non-extensiveness of the reaction.
Phosphorus (P) is an important element for the chemical evolution of galaxies and many kinds of biochemical reactions. Phosphorus is one of the crucial chemical compounds in the formation of life on our planet. In an interstellar medium, phosphine (PH$_{3}$) is a crucial biomolecule that plays a major role in understanding the chemistry of phosphorus-bearing molecules, particularly phosphorus nitride (PN) and phosphorus monoxide (PO), in the gas phase or interstellar grains. We present the first confirmed detection of phosphine (PH$_{3}$) in the asymptotic giant branch (AGB) carbon-rich star IRC+10216 using the Atacama Large Millimeter/Submillimeter Array (ALMA) band 6. We detect the $J$ = 1$_{0}$$-$0$_{0}$ rotational transition line of PH$_{3}$ with a signal-to-noise ratio (SNR) of $\geq$3.5$σ$. This is the first confirmed detection of phosphine (PH$_{3}$) in the ISM. Based on LTE spectral modelling, the column density of PH$_{3}$ is (3.15$\pm$0.20)$\times$10$^{15}$ cm$^{-2}$ at an excitation temperature of 52$\pm$5 K. The fractional abundance of PH$_{3}$ with respect to H$_{2}$ is (8.29$\pm$1.37)$\times$10$^{-8}$. We also discuss the possible formation pathways of PH$_{3}$ and we claim that PH$_{3}$ may be created via the hydrogenation of PH$_{2}$ on the grain surface of IRC+10216.
Porous CeTi2O6 brannerite is synthesized with high specific surface area and pore volume and exhibits good uranyl adsorption capacity. The material possesses high portion of mesopores facilitating fast uranyl adsorption.
In this paper, we study the electrostatics of pH-responsive polyelectrolyte-grafted spherical particles by using a strong stretching theory that takes into account the excluded volume interaction and the density of chargeable sites on the polyelectrolyte molecules. Based on the free energy formalism, we obtain self-consistent field equations for determining the structure and electrostatics of spherical polyelectrolyte brushes. First, we find that the smaller the radius of the inner core, the longer the height of the polyelectrolyte brush. Then, we also prove that an increase in excluded volume interaction yields an swelling of the polyelectrolyte brush height. In addition, we demonstrate how the effect of pH, bulk ionic concentration, and lateral separation between adjacent polyelectrolyte chains on the electrostatic properties of a spherical polyelectrolyte brush is affected by the radius of inner core, the excluded volume interaction and the chargeable site density.
In this work, we present an overview of the phaseless auxiliary-field quantum Monte Carlo (ph- AFQMC) approach from a computational quantum chemistry perspective, and present a numerical assessment of its performance on main group chemistry and bond-breaking problems with a total of 1004 relative energies. While our benchmark study is somewhat limited, we make recommendations for the use of ph-AFQMC for general main-group chemistry applications. For systems where single determinant wave functions are qualitatively accurate, we expect the accuracy of ph-AFQMC in conjunction with a single determinant trial wave function to be between that of coupled-cluster with singles and doubles (CCSD) and CCSD with perturbative triples (CCSD(T)). For these applications, ph-AFQMC should be a method of choice when canonical CCSD(T) is too expensive to run. For systems where multi-reference (MR) wave functions are needed for qualitative accuracy, ph-AFQMC is far more accurate than MR perturbation theory methods and competitive with MR configuration interaction (MRCI) methods. Due to the computational efficiency of ph-AFQMC compared to MRCI, we recommended ph-AFQMC as a method of choice for handling dynamic correlation in MR problems. We conclude with a discussion of important directions for future development of the ph-AFQMC approach.
Mohammad Ali Vakili, Morteza Sadeghi, Mohammad Hassan Saidi
et al.
In the present study, the ionic transport and selectivity of electrokinetically-driven flow of power-law fluids in a long pH-regulated rectangular nanochannel are analyzed. The electrical potential and momentum equations are numerically solved through a finite difference procedure for a non-uniform grid. Non-linear Poisson-Boltzmann equation along with the association/dissociation reactions on the surface is considered. In addition, numerical simulations with the finite element method in 3D space are performed to compare the results with those obtained from 2D analysis. Moreover, an analytical solution under Debye-Hückel approximation for the limiting case of a slit nanochannel is derived and its results are compared with those obtained from numerical simulations. It is shown that the channel aspect ratio can influence all the physicochemical parameters. It is observed that the mean velocity and the convective ionic conductance are strong descending functions of the flow behavior index. By investigating the non-Newtonian fluid behavior effect, it is revealed that its impact on the ionic conductance becomes significant at high values of the solution pH and its variation can alter the anionic transport direction inside the nanochannel. Moreover, it is shown the flow behavior index can strongly influence the ion selectivity of the nanochannel and its variation can be used to let the selectivity go through its maximum as a function of pH.
The heterogeneous oxidation reaction of single aqueous ascorbic acid (AH$_2$) aerosol particles with gas-phase ozone was investigated in this study utilizing aerosol optical tweezers with Raman spectroscopy. The measured liquid-phase bimolecular rate coefficients of the AH$_2$ + O$_3$ reaction exhibit a significant pH dependence, and the corresponding values at ionic strength 0.2 M are $(3.1 \pm 2.0) \times 10^5$ M$^{-1}$s$^{-1}$ and $(1.2 \pm 0.6) \times 10^7$ M$^{-1}$s$^{-1}$ for pH $\approx$ 2 and 6, respectively. These results measured in micron-sized droplets agree with those from previous bulk measurements, indicating that the observed aerosol reaction kinetics can be solely explained by liquid phase diffusion and AH$_2$ + O$_3$ reaction. Furthermore, the results indicate that high ionic strengths could enhance the liquid-phase rate coefficients of the AH$_2$ + O$_3$ reaction. The results also exhibit a negative ozone pressure dependence that can be rationalized in terms of a Langmuir-Hinshelwood type mechanism for the heterogeneous oxidation of AH$_2$ aerosol particles by gas-phase ozone. The results of the present work imply that in acidified airway-lining fluids the antioxidant ability of AH$_2$ against atmospheric ozone will be significantly suppressed.
Together with experimental data, theoretically predicted dipole moments represent a valuable tool for different branches in the chemical and physical sciences. With the diversity of levels of theory and basis sets available, a reliable combination must be carefully chosen in order to achieve accurate predictions. In a recent publication (arXiv:1709.05075 [physics.chem-ph]), Hait and Head-Gordon took a first step in this regard by providing recommendations on the best density functionals suitable for these purposes. However, no extensive study has been performed to provide recommendations on the basis set choice. Here, we shed some light into this matter by evaluating the performance of 38 general-purpose basis sets of single up to triple zeta-quality, when coupled with nine different levels of theory, in the computation of dipole moments. The calculations were performed on a data set with 114 small molecules containing second- and third-row elements. We based our analysis in regularised root mean square errors (regularised RMSE) as this procedure ensures relative errors for ionic species and absolute errors for species with small dipole moment values. Our results indicate that the best compromise between accuracy and computational efficiency is achieved by performing the computations with an augmented double zeta-quality basis set (i.e. aug-pc-1, aug-pcseg-1, aug-cc-pVDZ) together with a hybrid functional (e.g. wB97X-V, SOGGA11-X). Augmented triple-zeta basis sets could enhance the accuracy of the computations, but the computational cost of introducing such a basis set is substantial compared with the small improvement provided. These findings also highlight the crucial role that augmentation of the basis set with diffuse functions on both hydrogen and non-hydrogen atoms plays in the computation of dipole moments.
In this work, we develop an extended uniform potential (UP) model for a membrane nanopore by including two different charging mechanisms of the pore walls, namely by electronic charge and by chemical charge. These two charging mechanisms will generally occur in polymeric membranes with conducting agents, or membranes made of conducting materials like carbon nanotubes with surface ionizable groups. The electronic charge redistributes along the pore in response to the gradient of electric potential in the pore, while the chemical charge depends on the local pH via a Langmuir-type isotherm. The extended UP model shows good agreement with experimental data for membrane potential measured at zero current condition. When both types of charge are present, the ratio of the electronic charge to the chemical charge can be characterized by the dimensionless number of surface groups and the dimensionless capacitance of the dielectric Stern layer. The performance of the membrane pore in converting osmotic energy from a salt concentration difference into electrical power can be improved by tuning the electronic charge.