Water model
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Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields Open
Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the …
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Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions Open
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review th…
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Molecular Dynamics Simulations of Membrane Permeability Open
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydro…
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A force field of Li+, Na+, K+, Mg2+, Ca2+, Cl−, and SO42− in aqueous solution based on the TIP4P/2005 water model and scaled charges for the ions Open
In this work, a force field for several ions in water is proposed. In particular, we consider the cations Li+, Na+, K+, Mg2+, and Ca2+ and the anions Cl− and SO42−. These ions were selected as they appear in the composition of seawater, an…
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Water Dielectric Effects in Planar Confinement Open
We investigate the dielectric profile of water confined between two planar polar walls using atomistic molecular dynamics simulations. For a water slab thickness below 1 nm the dielectric response is highly asymmetric: while the parallel c…
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Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules Open
Molecular dynamics simulations have been performed to compute the solvation free energy and the octanol/water partition coefficients for a challenging set of selected organic molecules, characterized by the simultaneous presence of functio…
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CHARMM TIP3P Water Model Suppresses Peptide Folding by Solvating the Unfolded State Open
The accuracy of molecular dynamics simulations depends on the underlying force field, defined by the form and parametrization of the interparticle potential functions and the water model. The treatment of the solvent is crucial in molecula…
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Ab Initio Simulations of Water/Metal Interfaces Open
Structures and processes at water/metal interfaces play an important technological role in electrochemical energy conversion and storage, photoconversion, sensors, and corrosion, just to name a few. However, they are also of fundamental si…
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X-ray and Neutron Scattering of Water Open
This review article focuses on the most recent advances in X-ray and neutron scattering studies of water structure, from ambient temperature to the deeply supercooled and amorphous states, and of water diffusive and collective dynamics, in…
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Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models Open
Monovalent ions play significant roles in various biological and material systems. Recently, four new water models (OPC3, OPC, TIP3P-FB, and TIP4P-FB), with significantly improved descriptions of condensed phase water, have been developed.…
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Machine learning potentials for complex aqueous systems made simple Open
Simulation techniques based on accurate and efficient representations of potential energy surfaces are urgently needed for the understanding of complex aqueous systems such as solid-liquid interfaces. Here, we present a machine learning fr…
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Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water Open
Partition coefficients describe how a solute is distributed between two immiscible solvents. They are used in drug design as a measure of a solute's hydrophobicity and a proxy for its membrane permeability. We calculate partition coefficie…
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Signatures of a liquid–liquid transition in an ab initio deep neural network model for water Open
Significance Water is central across much of the physical and biological sciences and exhibits physical properties that are qualitatively distinct from those of most other liquids. Understanding the microscopic basis of water’s peculiar pr…
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A physically constrained classical description of the homogeneous nucleation of ice in water Open
Liquid water can persist in a supercooled state to below 238 K in the Earth’s atmosphere, a temperature range where homogeneous nucleation becomes increasingly probable. However, the rate of homogeneous ice nucleation in supercooled water …
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Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models Open
Divalent metal ions play important roles in biological and materials systems. Molecular dynamics simulation is an efficient tool to investigate these systems at the microscopic level. Recently, four new water models (OPC3, OPC, TIP3P-FB, a…
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Two-structure thermodynamics for the TIP4P/2005 model of water covering supercooled and deeply stretched regions Open
One of the most promising frameworks for understanding the anomalies of cold and supercooled water postulates the existence of two competing, interconvertible local structures. If the non-ideality in the Gibbs energy of mixing overcomes th…
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Temperature-dependent vibrational spectra and structure of liquid water from classical and quantum simulations with the MB-pol potential energy function Open
The structure of liquid water as a function of temperature is investigated through the modeling of infrared and Raman spectra along with structural order parameters calculated from classical and quantum molecular dynamics simulations with …
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Understanding each other's models: an introduction and a standard representation of 16 global water models to support intercomparison, improvement, and communication Open
Global water models (GWMs) simulate the terrestrial water cycle on the global scale and are used to assess the impacts of climate change on freshwater systems. GWMs are developed within different modelling frameworks and consider different…
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Cavity molecular dynamics simulations of liquid water under vibrational ultrastrong coupling Open
Significance Strong coupling between a vibrational molecular peak and a cavity mode is known to lead to interesting spectroscopic features and even the modification of ground-state chemistry from small molecules to enzyme. Here, we develop…
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Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties Open
Metal cations are essential in many vital processes. In order to capture the role of different cations in all-atom molecular dynamics simulations of biological processes, an accurate parametrization is crucial. Here, we develop force field…
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Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations Open
Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this co…
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Pressure dependence of viscosity in supercooled water and a unified approach for thermodynamic and dynamic anomalies of water Open
Significance Commuting during rush hours teaches us that the denser the crowd, the slower the motion. Liquids follow this law, except water below ambient temperature: Increasing density decreases viscosity! This anomaly witnesses the progr…
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Long-Term Stability of Different Kinds of Gas Nanobubbles in Deionized and Salt Water Open
Nanobubbles have many potential applications depending on their types. The long-term stability of different gas nanobubbles is necessary to be studied considering their applications. In the present study, five kinds of nanobubbles (N2, O2,…
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Enhancement and maximum in the isobaric specific-heat capacity measurements of deeply supercooled water using ultrafast calorimetry Open
Significance The importance of molecular understanding of the structure, dynamics. and properties of liquid water is recognized in many scientific disciplines. Here, we study experimentally the structure and thermodynamics of bulk liquid w…
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Temperature Dependence of Homogeneous Nucleation in Ice Open
Ice nucleation is a process of great relevance in physics, chemistry, technology, and environmental sciences; much theoretical effort has been devoted to its understanding, but it still remains a topic of intense research. We shed light on…
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Water Structure, Dynamics, and Sum-Frequency Generation Spectra at Electrified Graphene Interfaces Open
The properties of water at an electrified graphene electrode are studied via classical molecular dynamics simulations with a constant potential approach. We show that the value of the applied electrode potential has dramatic effects on the…
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Anomalies and Local Structure of Liquid Water from Boiling to the Supercooled Regime as Predicted by the Many-Body MB-pol Model Open
For the past 50 years, researchers have sought molecular models that can accurately reproduce water's microscopic structure and thermophysical properties across broad ranges of its complex phase diagram. Herein, molecular dynamics simulati…
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FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules Open
Accurate force‐field (FF) parameters are key to reliable prediction of properties obtained from molecular modeling (MM) and molecular dynamics (MD) simulations. With ever‐widening applicability of MD simulations, robust parameters need to …
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Mode coupling theory and fragile to strong transition in supercooled TIP4P/2005 water Open
We study by molecular dynamics simulations supercooled water with the TIP4P/2005 potential. This model is able to predict many properties of water in a large range of the thermodynamic space in agreement with experiments. We explore the dy…
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Martini 3 Coarse-Grained Force Field for Carbohydrates Open
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the p…