Reply to the ‘Comment on “Simulations of ionization equilibria in weak polyelectrolyte solutions and gels”’ by J. Landsgesell, L. Nová, O. Rud, F. Uhlík, D. Sean, P. Hebbeker, C. Holm and P. Košovan, <i>Soft Matter</i>, 2019, <b>15</b>, 1155–1185

Košovan, Peter; Landsgesell, Jonas; Nová, Lucie; Uhlı́k, Filip; Beyer, David; Blanco, Pablo M.; Staňo, Roman; Holm, Christian

doi:10.1039/d3sm00155e

Cited by 4 publications

(4 citation statements)

References 11 publications

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“…Furthermore, this “neutralizer” ion should not be confused with explicit

ions since the concentration of neutralizer ions does not necessarily correspond with the one corresponding to the pH-value. In addition, one needs to correct Equation ( 64 ) by the excess chemical potential of the neutralizer ion [ 164 , 165 ]. Otherwise, one obtains deviations that are asymmetric depending whether a cation or an anion is used as neutralizer ion.…”

Section: Computer Simulations Of Weak Polyelectrolytes At Constant Phmentioning

confidence: 99%

“…Examples of such systems are weak polyelecrolyte hydrogels [ 169 , 170 ], coacervates of weak polyelectrolytes [ 279 , 280 , 281 , 282 , 283 ] and concentrated solutions of proteins under ultrafiltration–diafiltration processes [ 236 ]. In such systems, CR is coupled with the Donnan potential generated between the two phases producing a complicated feedback loop [ 38 , 165 ]. Recent advances in simulation techniques permitting to model those systems, such as the Grand-Reaction ensemble method, open exciting new possibilities [ 38 , 166 ].…”

Section: Outlooksmentioning

confidence: 99%

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Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes

et al. 2023

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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.

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“…Furthermore, this “neutralizer” ion should not be confused with explicit

Section: Computer Simulations Of Weak Polyelectrolytes At Constant Phmentioning

confidence: 99%

Section: Outlooksmentioning

confidence: 99%

Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes

et al. 2023

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“…Within the mean-field picture, the degree of ionization, α, can be described by the Henderson–Hasselbalch equation, augmented by an additional electrostatic term − normalpH − normalp K normalA = log 10 nobreak0em.25em⁡ 1 − α α + z e ψ k normalB T nobreak0em0.25em⁡ ln 10 where e is the elementary charge, z = ±1 is the valency of the ionized group, and ψ is the local electrostatic potential. In the absence of interactions (ideal gas limit), ψ = 0; therefore, 50% of the groups in the molecules are ionized (α = 0.5) at pH = p K A .…”

Section: Introductionmentioning

confidence: 99%

“…The shift of the effective p K A then follows as p K A eff = p K A + ( zeψ )/( k B T ln10). 52 In our previous studies, 54 − 59 the above mechanism of shifting the effective p K A has been termed the polyelectrolyte effect . The latter has been contrasted with the Donnan effect , caused by uneven partitioning of H + ions between different phases in two-phase systems, resulting in different pH values in these two phases.…”

Section: Introductionmentioning

confidence: 99%

Charge Regulation Triggers Condensation of Short Oligopeptides to Polyelectrolytes

Pineda,

Staňo,

Murmiliuk

et al. 2024

JACS Au

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Electrostatic interactions between charged macromolecules are ubiquitous in biological systems, and they are important also in materials design. Attraction between oppositely charged molecules is often interpreted as if the molecules had a fixed charge, which is not affected by their interaction. Less commonly, charge regulation is invoked to interpret such interactions, i.e., a change of the charge state in response to a change of the local environment. Although some theoretical and simulation studies suggest that charge regulation plays an important role in intermolecular interactions, experimental evidence supporting such a view is very scarce. In the current study, we used a model system, composed of a long polyanion interacting with cationic oligolysines, containing up to 8 lysine residues. We showed using both simulations and experiments that while these lysines are only weakly charged in the absence of the polyanion, they charge up and condense on the polycations if the pH is close to the pK a of the lysine side chains. We show that the lysines coexist in two distinct populations within the same solution: (1) practically nonionized and free in solution; (2) highly ionized and condensed on the polyanion. Using this model system, we demonstrate under what conditions charge regulation plays a significant role in the interactions of oppositely charged macromolecules and generalize our findings beyond the specific system used here.

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pyMBE: The Python-based molecule builder for ESPResSo

Beyer,

Torres,

Pineda

et al. 2024

The Journal of Chemical Physics

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We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application to design custom coarse-grained (CG) models, as well as pre-defined models of polyelectrolytes, peptides, and globular proteins in the Extensible Simulation Package for Research on Soft Matter (ESPResSo). The Python interface of ESPResSo offers a flexible framework, capable of building custom CG models from scratch. As a downside, building CG models from scratch is prone to mistakes, especially for newcomers in the field of CG modeling, or for molecules with complex architectures. The pyMBE module builds CG models in ESPResSo using a hierarchical bottom-up approach, providing a robust tool to automate the setup of CG models and helping new users prevent common mistakes. ESPResSo features the constant pH (cpH) and grand-reaction (G-RxMC) methods, which have been designed to study chemical reaction equilibria in macromolecular systems with many reactive species. However, setting up these methods for systems, which contain several types of reactive groups, is an error-prone task, especially for beginners. The pyMBE module enables the automatic setup of cpH and G-RxMC simulations in ESPResSo, lowering the barrier for newcomers and opening the door to investigate complex systems not studied with these methods yet. To demonstrate some of the applications of pyMBE, we showcase several case studies where we successfully reproduce previously published simulations of charge-regulating peptides and globular proteins in bulk solution and weak polyelectrolytes in dialysis. The pyMBE module is publicly available as a GitHub repository (https://github.com/pyMBE-dev/pyMBE), which includes its source code and various sample and test scripts, including the ones that we used to generate the data presented in this article.

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Reply to the ‘Comment on “Simulations of ionization equilibria in weak polyelectrolyte solutions and gels”’ by J. Landsgesell, L. Nová, O. Rud, F. Uhlík, D. Sean, P. Hebbeker, C. Holm and P. Košovan, Soft Matter, 2019, 15, 1155–1185

Abstract: A defence and further discussions are provided for a recent review on simulations of ionization equilibria which address in detail the three main points made in the Comment.

Cited by 4 publications

References 11 publications

Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes

Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes

Charge Regulation Triggers Condensation of Short Oligopeptides to Polyelectrolytes

pyMBE: The Python-based molecule builder for ESPResSo

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