Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes

Klug, Joaquín; Triguero, Carles; Pópolo, Mario G. Del; Tribello, Gareth A.

doi:10.1021/acs.jpcb.8b03661

Cited by 8 publications

(8 citation statements)

References 54 publications

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“…In umbrella sampling (Torrie and Valleau, 1977), the reaction coordinate space is mapped on a set of consecutive quasi-equilibrium simulations, with the reaction coordinates restrained at a different value in each simulation. Quasi-equilibrium methods (Sakaguchi and Morita, 2012) provide a free-energy estimate that artificially averages out effects of surface fluctuations (as a result of the method used to average the force as a function of the reaction coordinate) (Darvas et al, 2013;Braga et al, 2016;Klug et al, 2018) whose spatial and temporal scales are similar to those of a typical atmospheric water uptake event.…”

Section: Technical Backgroundmentioning

confidence: 99%

“…Thermal fluctuations are not accounted for by traditional surface definitions and cause artificial smoothing of the surface and systematic errors in the selection of surface molecules (Bartók- Pártay et al, 2008;Jorge et al, 2010). Intrinsic surface analysis -i.e., decoupling surface fluctuations from the interfacial properties (Appendix A)of molecular simulation trajectories is necessary to resolve the effect of capillary waves on density (Jorge et al, 2010) and free-energy profiles (Darvas et al, 2013;Braga et al, 2016;Klug et al, 2018). Results are sharper and contain features which are smoothed out by fluctuations using traditional surface definitions.…”

Section: Intrinsic Density Profilesmentioning

confidence: 99%

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Molecular-scale description of interfacial mass transfer in phase-separated aqueous secondary organic aerosol

2021

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Abstract. Liquid–liquid phase-separated (LLPS) aerosol particles are known to exhibit increased cloud condensation nuclei (CCN) activity compared to well-mixed ones due to a complex effect of low surface tension and non-ideal mixing. The relation between the two contributions as well as the molecular-scale mechanism of water uptake in the presence of an internal interface within the particle is to date not fully understood. Here we attempt to gain understanding in these aspects through steered molecular dynamics simulation studies of water uptake by a vapor–hydroxy-cis-pinonic acid–water double interfacial system at 200 and 300 K. Simulated free-energy profiles are used to map the water uptake mechanism and are separated into energetic and entropic contributions to highlight its main thermodynamic driving forces. Atmospheric implications are discussed in terms of gas–particle partitioning, intraparticle water redistribution timescales and water vapor equilibrium saturation ratios. Our simulations reveal a strongly temperature-dependent water uptake mechanism, whose most prominent features are determined by local extrema in conformational and orientational entropies near the organic–water interface. This results in a low core uptake coefficient (ko/w=0.03) and a concentration gradient of water in the organic shell at the higher temperature, while entropic effects are negligible at 200 K due to the association-entropic-term reduction in the free-energy profiles. The concentration gradient, which results from non-ideal mixing – and is a major factor in increasing LLPS CCN activity – is responsible for maintaining liquid–liquid phase separation and low surface tension even at very high relative humidities, thus reducing critical supersaturations. Thermodynamic driving forces are rationalized to be generalizable across different compositions. The conditions under which single uptake coefficients can be used to describe growth kinetics as a function of temperature in LLPS particles are described.

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Section: Technical Backgroundmentioning

confidence: 99%

Section: Intrinsic Density Profilesmentioning

confidence: 99%

Molecular-scale description of interfacial mass transfer in phase-separated aqueous secondary organic aerosol

2021

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“…A recently developed alternative CV called 'distance from contour' can be defined in terms of the distance to both the closest and furthest edges of the membrane, which accounts for local fluctuations in the shape of the membrane due to the SMMI [146]. Additionally, there is a tendency to assume a symmetric behaviour of the SMMI along the COM distance across the entire membrane, and thus many studies only calculate the free energy for windows from solution to the COM of the lipid bilayer (i.e.…”

Section: Common Quantities In Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes

et al. 2020

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Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other type of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.

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“…In umbrella sampling (Torrie and Valleau, 1977), the reaction coordinate space is mapped in a set of consecutive quasi-equilibrium simulations, with the reaction coordinates restrained at a different value in each simulation. Quasi-equilibrium methods (Sakaguchi and Morita, 2012) provide a free energy estimate that artificially averages out effects of surface fluctuations (as a result of the method used to average the force as a function of the reaction coordinate) (Darvas et al, 2013;Braga et al, 2016;Klug et al, 2018) whose spatial and temporal scales are similar to those of a typical atmospheric water uptake event.…”

Section: Technical Backgroundmentioning

confidence: 99%

“…decoupling surface fluctuations from the determining interfacial properties (Appendix A) -of molecular simulation trajectories is necessary to resolve the effect of capillary waves on density (Jorge et al, 2010) and free energy profiles (Darvas et al, 2013;Braga et al, 2016;Klug et al, 2018) results are sharper and contain features which are smoothed out by fluctuations using traditional surface definitions. In this work, intrinsic analysis is limited to the selection of surface molecules and the calculation of density profiles anchored to the fluctuating surface by the ITIM algorithm (Sega et al, 2018), which allows to establish qualitative connections between the free energy profiles and the local perturbations of solution structure and thermodynamic properties in the vicinity of interfaces.…”

Section: Intrinsic Density Profilesmentioning

confidence: 99%

Molecular scale description of interfacial mass transfer in phase separated aqueous secondary organic aerosol

Lbadaoui-Darvas

Takahama

Nenes

2021

Preprint

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Abstract. Liquid-liquid phase separated (LLPS) aerosol particles are known to exhibit increased cloud condensation nuclei (CCN) activity compared to well mixed ones due to a complex effect of low surface tension and non-ideal mixing. The relation between the two contributions as well as the molecular scale mechanism of water uptake in the presence of an internal interface within the particle is to date not fully understood. Here we present steered molecular dynamics simulation studies of water uptake by a vapor/hydroxi-cis-pinonic acid/water double interfacial system at 200 K and 300 K. Simulated free energy profiles are used to map the water uptake mechanism and are decomposed into energetic and entropic contributions to highlight its main thermodynamic driving forces. Atmospheric implications are discussed in terms of gas/particle partitioning, intraparticle water redistribution timescales, and equilibrium saturation ratios of water vapor. Our simulations reveal a strongly temperature-dependent water uptake mechanism, whose most prominent features are determined by local extrema in conformational and orientational entropies near the organic/water interface which result in a reduced core uptake coefficient (ko/w = 0.05) and a concentration gradient of water in the organic shell at the higher temperature, while their effect is negligible at 200 K due to the explicit temperature dependence of entropic terms in the free energy profiles. The concentration gradient, which is a molecular level manifestation of non-ideal mixing – suspected to be a major factor to increase LLPS CCN activity – is responsible for maintaining LLPS and low surface tension even at very high relative humidities, thus reducing critical supersaturations. Thermodynamic driving forces are rationalised to be generalizable across different compositions. The conditions under which single uptake coefficients can be used to to describe growth kinetics as a function of temperature in LLPS particles are described.

show abstract

Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes

Cited by 8 publications

References 54 publications

Molecular-scale description of interfacial mass transfer in phase-separated aqueous secondary organic aerosol

Molecular-scale description of interfacial mass transfer in phase-separated aqueous secondary organic aerosol

Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes

Molecular scale description of interfacial mass transfer in phase separated aqueous secondary organic aerosol

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