Using Car-Parrinello simulations and microscopic order descriptors to reveal two locally favored structures with distinct molecular dipole moments and dynamics in ambient liquid water

Skarmoutsos, Ioannis; Franzese, Giancarlo; Guàrdia, E.

doi:10.1016/j.molliq.2022.119936

Cited by 8 publications

(5 citation statements)

References 74 publications

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“…As shown in Figure 3f, the average number of hydrogen bonds, which one water molecule forms, increases as the water content increases. Based on the recent observation that bulk water molecules forming more hydrogen bonds and with more tetrahedral order have a larger dipole moment than those with fewer hydrogen bonds, 26 our data suggest that the increase in the polarity of water is caused by the rise in the number of hydrogen bonds.…”

Section: Resultssupporting

confidence: 55%

Structure and Diffusive Properties of Water in Polymer Hydrogels

et al. 2022

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To investigate the diffusive properties of water in hydrogels, ab initio molecular orbital and molecular dynamics calculations of poly-N,N-dimethylacrylamide-water systems were performed. The results show that the mean diffusion coefficient of water drastically decreases in the middle dehydration stage. In this stage, the mobilities of water are restrained because part of the water forms hydrogen bonds to bind polymer chains due to a glass transition. In addition to the three well-known types of water (i.e., bound, intermediate, and free water) around hydrophilic polymers in hydrogels, our results suggest that the intermediate water can be further classified into two types: first and second intermediate water. The bound and first intermediate water acts as a cross-linker between polymer chains, even if the polymer does not form intra-or intermolecular bonds itself. The diffusive properties of water might have important implications for the interpretation of properties of polymer hydrogels.

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Section: Resultssupporting

confidence: 55%

Structure and Diffusive Properties of Water in Polymer Hydrogels

et al. 2022

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“…It favors the formation of a low-density (tetrahedral) local structure in liquid water even at ambient conditions. 72 In classical atomistic potentials, this term is modeled with a long-range polarizable dipolar interaction. However, recent calculations, based on polarizable models including the MB-pol potential, [73][74][75][76] show that it can be approximated with a short-range 5-body interaction within the first coordination shell of a water molecule.…”

Section: Modelmentioning

confidence: 99%

Intrinsically disordered protein’s coil-to-globule transition and adsorption onto a hydrophobic surface under different conditions

Fauli

Bianco²,

Franzese

2023

Preprint

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Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) can modulate cellular responses to environmental conditions by undergoing coil-to-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we use Monte Carlo calculations of a model incorporating water's effects on the system's free energy to investigate how an IDP responds to a hydrophobic surface under different conditions. We show that a slit pore confinement without top-down symmetry enhances the unfolding and adsorption of the IDP in both random coil and globular states. Moreover, we demonstrate that the hydration water modulates this behavior depending on the thermodynamic parameters. Our findings provide insights into how IDPs and IDRs can sense and adjust to external stimuli such as nanointerfaces or stresses.

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“…The last term in the Hamiltonian, − J σ N σ , accounts for the many-body term that can be calculated by the ab initio methods. It favors the formation of a low-density (tetrahedral) local structure in liquid water even at ambient conditions . In classical atomistic potentials, this term is modeled with a long-range polarizable dipolar interaction.…”

Section: Modelmentioning

confidence: 99%

“…It favors the formation of a low-density (tetrahedral) local structure in liquid water even at ambient conditions. 76 In classical atomistic potentials, this term is modeled with a long-range polarizable dipolar interaction. However, recent calculations, based on polarizable models including the MB-pol potential, 77 − 80 show that it can be approximated with a short-range 5-body interaction within the first coordination shell of a water molecule.…”

Section: Modelmentioning

confidence: 99%

Hydrophobic Homopolymer’s Coil–Globule Transition and Adsorption onto a Hydrophobic Surface under Different Conditions

Durà

Bianco²,

Franzese

2023

J. Phys. Chem. B

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Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil−globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we use Monte Carlo calculations of a coarse-grained model incorporating water's effects on the system's free energy. Following previous studies, we modeled an unstructured protein as a polymer chain. Because we are interested in investigating how it responds to thermodynamic changes near a hydrophobic surface under different conditions, we chose an entirely hydrophobic sequence to maximize the interaction with the interface. We show that a slit pore confinement without top-down symmetry enhances the unfolding and adsorption of the chain in both random coil and globular states. Moreover, we demonstrate that the hydration water modulates this behavior depending on the thermodynamic parameters. Our findings provide insights into how homopolymers and possibly unstructured proteins can sense and adjust to external stimuli such as nanointerfaces or stresses.

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Using Car-Parrinello simulations and microscopic order descriptors to reveal two locally favored structures with distinct molecular dipole moments and dynamics in ambient liquid water

Cited by 8 publications

References 74 publications

Structure and Diffusive Properties of Water in Polymer Hydrogels

Structure and Diffusive Properties of Water in Polymer Hydrogels

Intrinsically disordered protein’s coil-to-globule transition and adsorption onto a hydrophobic surface under different conditions

Hydrophobic Homopolymer’s Coil–Globule Transition and Adsorption onto a Hydrophobic Surface under Different Conditions

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