Site Correlations, Capacitance, and Polarizability From Protein Protonation Fluctuations

Patchy Charge Distribution Affects the pH in Protein Solutions during Dialysis

When using dialysis ultra- or diafiltration to purify protein solutions, a dialysis buffer in the permeate is employed to set the pH in the protein solution. Failure to achieve the target pH may cause undesired precipitation of the valuable product. However, the pH in the permeate differs from that in the retentate, which contains the proteins. Experimental optimization of the process conditions is time-consuming and expensive, while accurate theoretical predictions still pose a major challenge. Current models of dialysis account for the Donnan equilibrium, acid-base properties, and ion-protein interactions, but they neglect the patchy distribution of ionizable groups on the proteins and its impact on the solution properties. Here, we present a simple computational model of a colloidal particle with weakly acidic sites on the surface, organized in patches. This minimalistic model allows systematic variation of the relevant parameters, while simultaneously demonstrating the essential physics governing the acid-base equilibria in protein solutions. Using molecular simulations in the Grand-Reaction ensemble, we demonstrate that interactions between ionizable sites significantly affect the nanoparticle charge and thereby contribute to pH difference between the permeate and retentate. We show that the significance of this contribution increases if the ionizable sites are located on a smaller patch. Protein solutions are governed by the same physics as our simple model. In this context, our results show that models which aim to quantitatively predict the pH in protein solutions during dialysis need to account for the patchy distribution of ionizable sites on the protein surface.

Electrostatic and Electronic Effects on Doped Nickel Oxide Nanofilms for Water Oxidation

An ideal water-splitting electrocatalyst is inexpensive, abundant, highly active, stable, selective, and durable. The anodic oxygen evolution reaction (OER) is the main bottleneck for H2 production with a complex and not fully resolved mechanism, slow kinetics, and high overpotential. Nickel oxide-based catalysts (NiOx) are highly active and cheaper than precious metal catalysts. However, rigorous catalyst tests and DFT calculations are still needed to rationally optimize NiOx catalysts. In this work, we combine plasma-enhanced atomic layer deposition (PE-ALD) and density functional theory (DFT) to address the role of dopants in promoting NiOx OER activity. Ultrathin films of NiOx doped with Zn2+, Al3+, and Sn4+ presented improved intrinsic activity, stability, and durability for the OER. The results show a low to high catalytic performance of ZnNiOx < NiOx < AlNiOx < SnNiOx, which we attribute to an increase in the concentration of valence band (VB) holes combined with conduction band (CB) electron conductivity, characterized by electrochemical impedance spectroscopy (EIS). The influence of doping on the electronic structure and catalytic activity was investigated using advanced characterization techniques and density functional theory (DFT) calculations (PEB0/pob-TZVP). DFT complements the experimental results, showing that the dopant charge states and orbital hybridization enhance the OER by improving the charge carrier concentration and mobility, thus allowing optimal binding energies and charge dynamics and delocalization. Our findings demonstrate the potential of PE-ALD-doped nanofilms NiOx and DFT to rationally design and develop catalysts for sustainable energy applications.

Quantum Computer Simulation of Protein Protonation

In attempts to simulate the protonation of proteins, a major challenge is that the number of protonation states grows rapidly as a function (2N) of the number of protonation sites (N). Expression on the free energy of the protonation state as an N-site Ising model ─ using an empirical Generalized-Born model ─ allows a quantum computer to efficiently determine the important states at a given pH value and subsequently reconstruct the pH titration process at all sites. Compared with the exact results painstakingly obtained with classical computers, the results obtained using quantum computers show good agreement for staphylococcal nuclease and excellent agreement for α-lactalbumin. This work illustrates the effectiveness of quantum computers in sampling important physical states, which may be useful in attacking challenging biomolecular problems.

Charge fluctuations in charge-regulated systems: dependence on statistical ensemble

We investigate charge regulation of nanoparticles in concentrated suspensions, focusing on the effect of different statistical ensembles. We find that the choice of ensemble does not affect the mean charge of nanoparticles, but significantly alters the magnitude of its fluctuation. Specifically, we compared the behaviors of colloidal charge fluctuations in the semi-grand canonical and canonical ensembles and identified significant differences between the two. The choice of ensemble-whether the system is isolated or is in contact with a reservoir of acid and salt-will, therefore, affect the Kirkwood-Shumaker fluctuation-induced force inside concentrated suspensions. Our results emphasize the importance of selecting an appropriate ensemble that accurately reflects the experimental conditions when studying fluctuation-induced forces between polyelectrolytes, proteins, and colloidal particles in concentrated suspensions.

Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes

This article reviews the state of the art of the studies on charge regulation (CR) effects in flexible weak polyelectrolytes (FWPE). The characteristic of FWPE is the strong coupling of ionization and conformational degrees of freedom. After introducing the necessary fundamental concepts, some unconventional aspects of the the physical chemistry of FWPE are discussed. These aspects are: (i) the extension of statistical mechanics techniques to include ionization equilibria and, in particular, the use of the recently proposed Site Binding-Rotational Isomeric State (SBRIS) model, which allows the calculation of ionization and conformational properties on the same foot; (ii) the recent progresses in the inclusion of proton equilibria in computer simulations; (iii) the possibility of mechanically induced CR in the stretching of FWPE; (iv) the non-trivial adsorption of FWPE on ionized surfaces with the same charge sign as the PE (the so-called "wrong side" of the isoelectric point); (v) the influence of macromolecular crowding on CR.