Conformational transitions of a weak polyampholyte

Nair, Arun Kumar Narayanan; Uyaver, Şahin; Sun, Shuyu

doi:10.1063/1.4897161

Cited by 26 publications

(11 citation statements)

References 59 publications

(173 reference statements)

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“…The observed deviations from the ideal behaviour might seem rather small, however, it has been shown in previous qualitative studies that such effects can be boosted by using longer chains. [45][46][47]58 Thus, our results suggest a novel route to bottom-up engineering the ionisation response of peptides and weak ampholytes by choosing suitable pK A values of the side-chains and by optimising the sequence using numerical simulations. These simulations can be completed within a few hours of computer time (see ESI, Section 1.4).…”

Section: Discussionmentioning

confidence: 85%

“…Our model considers the ionisation response of these oligopeptides and its relation to molecular geometry and conformational flexibility, similar to earlier simulations of weak ampholytes. [45][46][47] However, it is presumably for the first time that such a model is used for one-to-one comparison of such simulations with experiments. Synthetic peptides are an ideal model system because they can be synthesized with a well-defined sequence, at sufficient purity, and with suitable combinations of pK A values.…”

Section: Introductionmentioning

confidence: 99%

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Quantitative Prediction of Charge Regulation in Oligopeptides

Lunkad¹,

Murmiliuk²,

Hebbeker³

et al. 2020

Preprint

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Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their ionisation response and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Differences in ionisation response between oligopeptides and monomeric amino acids showed that electrostatic interactions between weak acid and base side chains play a key role in oligopeptide ionisation, as predicted by our model. Moreover, by comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the ionisation response and electrophoretic mobilities of various peptide sequences. Ultimately, our model is the first step towards using predictive bottom-up design of responsive ampholytes to tailor their properties as a function of charge and pH.<br>

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Section: Discussionmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Quantitative Prediction of Charge Regulation in Oligopeptides

Lunkad¹,

Murmiliuk²,

Hebbeker³

et al. 2020

Preprint

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“…Our earlier studies have shown that Monte Carlo (MC) and molecular dynamics (MD) simulations are powerful tools to provide insight into the bulk and surface properties. − In this paper, we use computer simulations to study the adsorption and diffusion properties of methane and CO 2 in cross-linked polyethylene in the temperature range 300–600 K. We employ grand canonical Monte Carlo (GCMC) simulation method to calculate the adsorption isotherms, and MD simulations allow us to assess the dynamic properties of the system. In GCMC simulations, a rigid framework is usually employed to reduce the simulation time by avoiding the necessity of computing solid–solid interactions .…”

Section: Introductionmentioning

confidence: 99%

Adsorption and Diffusion of Methane and Carbon Dioxide in Amorphous Regions of Cross-Linked Polyethylene: A Molecular Simulation Study

Yang

Nair

Sun

2019

Ind. Eng. Chem. Res.

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We perform Monte Carlo (MC) and molecular dynamics (MD) simulations to study the adsorption and diffusion properties of methane and CO2 in cross-linked polyethylene in the temperature range 300–600 K. A hybrid MC/MD approach was used to incorporate the effects of framework flexibility and polymer swelling on the gas adsorption. The polymers show negligible swelling at the studied conditions. A nonmonotonic behavior of gas adsorption as a function of the cross-linking degree was obtained. Notably, a similar behavior was observed for the void fraction and pore diameters. This shows a direct correlation between gas adsorption and the pore characteristics of the cross-linked polymer network. Mobility of methane and carbon dioxide in the polymer matrix increases with temperature. Also, gas mobility decreases with increasing cross-linking degree, consistent with experiments. These results can be explained by the fact that the waiting time for a gas molecule in a cavity before the jump increases with decreasing temperature and increasing cross-linking degree. Interestingly, the activation energy for gas diffusion generally decreases with increasing cross-linking. This is possibly due to the fact that increasing the cross-linking degree leads to smaller pore sizes especially at high temperatures. Such a molecular-level understanding of adsorption and diffusion of gases in cross-linked polyethylene is important in improving the performance of polymer networks for potential applications in gas separation, barrier technology, and food packaging.

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“…Our previous studies have shown that molecular simulations are a useful approach to assess the surface and chemical interactions. ,− In this study, we employ grand canonical Monte Carlo (GCMC) calculations to acquire a molecular-level description of the effect of RH on H 2 O uptake by high-charge clays (Arizona-type montmorillonite) at 298.15 K. The simulation results of basal distances obtained from swelling free energy curves and of H 2 O uptake were applied to aid in the interpretation of experimental measurements ,, on high-charge montmorillonite clays. In addition, we performed molecular dynamics (MD) calculations to determine the mechanisms of water and ion diffusion in high-charge montmorillonite clays with varying RH.…”

Section: Introductionmentioning

confidence: 99%

Layer Charge Effects on Adsorption and Diffusion of Water and Ions in Interlayers and on External Surfaces of Montmorillonite

Yang

Nair

Sun

2019

ACS Earth Space Chem.

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Molecular simulations using classical force fields were performed to study the adsorption and diffusion properties of water and ions in the high-charge (Arizonatype) montmorillonite clays with varying relative humidity (RH) at 298.15 K. The simulation results of basal distances derived from swelling free energy curves and of water uptake are in good agreement with experiments. Overall, the simulated self-diffusion coefficients of the interlayer species are in reasonable agreement with experiments and lower than those estimated for the external surfaces. Influence of the magnitude of the layer charge was studied by comparing these simulation results with those obtained for the low-charge (Wyoming-type) montmorillonite clays. Most importantly, these comparisons confirm the experimental finding that the high-charge clay generally shifts swelling transitions toward lower RH values. Therefore, the adsorption and dynamics of water and ions are significantly different in the low-and high-charge clays near the transition RH values. We find that the amount of water in an interlayer hydration state is mostly independent of the layer charge, probably due to steric reasons. In contrast, the externally adsorbed water content increases with increasing layer charge. Furthermore, the mobility of water and ions is generally lower in the high-charge montmorillonite than in the corresponding low-charge system. However, mobility of cations in the mesopores of high-charge montmorillonite is typically higher than that of the corresponding low-charge system which might be attributed to the presence of the tetrahedral substitutions in the later case.

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Conformational transitions of a weak polyampholyte

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Cited by 26 publications

References 59 publications

Quantitative Prediction of Charge Regulation in Oligopeptides

Quantitative Prediction of Charge Regulation in Oligopeptides

Adsorption and Diffusion of Methane and Carbon Dioxide in Amorphous Regions of Cross-Linked Polyethylene: A Molecular Simulation Study

Layer Charge Effects on Adsorption and Diffusion of Water and Ions in Interlayers and on External Surfaces of Montmorillonite

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