scholarly journals Influence of effective polarization on ion and water interactions within a biomimetic nanopore

2021 ◽  
Author(s):  
Linda X Phan ◽  
Charlotte I Lynch ◽  
Jason Crain ◽  
Mark Sansom ◽  
Stephen J Tucker
Keyword(s):  
Ion Channels ◽  
Hydration Number ◽  
Hydration Shell ◽  
Md Simulations ◽  
Hydrophobic Region ◽  
Density Distributions ◽  
Energy Profiles ◽  
Hydrophobic Pore ◽  
Effective Polarization ◽  
Ion Effects

Interactions between ions and water at hydrophobic interfaces within ion channels and nanopores are suggested to play a key role in the movement of ions across biological membranes. Previous molecular dynamics (MD) simulations have shown that the affinity of polarizable anions to aqueous/hydrophobic interfaces can be markedly influenced by including polarization effects through an electronic continuum correction (ECC). Here, we designed a model biomimetic nanopore to imitate the polar pore openings and hydrophobic gating regions found in pentameric ligand-gated ion channels. MD simulations were then performed using both a non-polarizable force field and the ECC method to investigate the behavior of water, Na+ and Cl- ions confined within the hydrophobic region of the nanopore. Number density distributions revealed preferential Cl- adsorption to the hydrophobic pore walls, with this interfacial layer largely devoid of Na+. Free energy profiles for Na+ and Cl- permeating the pore also display an energy barrier reduction associated with the localization of Cl- to this hydrophobic interface, and the hydration number profiles reflect a corresponding reduction in the first hydration shell of Cl-. Crucially, these ion effects were only observed through inclusion of effective polarization which therefore suggests that polarizability may be essential for an accurate description for the behavior of ions and water within hydrophobic nanoscale pores, especially those that conduct Cl-.

scholarly journals CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

Geofluids ◽  
2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Yuan Mei ◽  
Weihua Liu ◽  
A. A. Migdiov ◽  
Joël Brugger ◽  
A. E. Williams-Jones
Keyword(s):  
Molecular Dynamics ◽  
Water Molecule ◽  
Ab Initio ◽  
Hydration Number ◽  
Hydration Shell ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Low Density ◽  
Fluid Density ◽  
Hydration Numbers

We investigated the hydration of the CuCl0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H2O-Cu-Cl]0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm3 (fH2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.

scholarly journals Confined Dynamics of Water in Transmembrane Pore of TRPV1 Ion Channel

2019 ◽  
Vol 20 (17) ◽  
pp. 4285
Author(s):  
Yury A. Trofimov ◽  
Nikolay A. Krylov ◽  
Roman G. Efremov
Keyword(s):  
Ion Channels ◽  
Transient Receptor Potential ◽  
3D Structure ◽  
Receptor Potential ◽  
Md Simulations ◽  
Transient Receptor Potential Vanilloid ◽  
Free Energy Barrier ◽  
Transmembrane Pores ◽  
Ion Conducting ◽  
Transient Receptor

Solvation effects play a key role in chemical and biological processes. The microscopic properties of water near molecular surfaces are radically different from those in the bulk. Furthermore, the behavior of water in confined volumes of a nanometer scale, including transmembrane pores of ion channels, is especially nontrivial. Knowledge at the molecular level of structural and dynamic parameters of water in such systems is necessary to understand the mechanisms of ion channels functioning. In this work, the results of molecular dynamics (MD) simulations of water in the pore and selectivity filter domains of TRPV1 (Transient Receptor Potential Vanilloid type 1) membrane channel are considered. These domains represent nanoscale volumes with strongly amphiphilic walls, where physical behavior of water radically differs from that of free hydration (e.g., at protein interfaces) or in the bulk. Inside the pore and filter domains, water reveals a very heterogeneous spatial distribution and unusual dynamics: It forms compact areas localized near polar groups of particular residues. Residence time of water molecules in such areas is at least 1.5 to 3 times larger than that observed for similar groups at the protein surface. Presumably, these water “blobs” play an important role in the functional activity of TRPV1. In particular, they take part in hydration of the hydrophobic TRPV1 pore by localizing up to six waters near the so-called “lower gate” of the channel and reducing by this way the free energy barrier for ion and water transport. Although the channel is formed by four identical protein subunits, which are symmetrically packed in the initial experimental 3D structure, in the course of MD simulations, hydration of the same amino acid residues of individual subunits may differ significantly. This greatly affects the microscopic picture of the distribution of water in the channel and, potentially, the mechanism of its functioning. Therefore, reconstruction of the full picture of TRPV1 channel solvation requires thorough atomistic simulations and analysis. It is important that the naturally occurring porous volumes, like ion-conducting protein domains, reveal much more sophisticated and fine-tuned regulation of solvation than, e.g., artificially designed carbon nanotubes.

scholarly journals Ab initio QM/MM MD simulations of the hydrated Ca2+ ion

2004 ◽  
Vol 76 (1) ◽  
pp. 37-47 ◽  
Author(s):  
C. F. Schwenk ◽  
B. M. Rode
Keyword(s):  
Density Functional ◽  
Hydration Shell ◽  
Md Simulations ◽  
Distribution Functions ◽  
Quantum Mechanical ◽  
Hartree Fock ◽  
Velocity Autocorrelation ◽  
Exchange Processes ◽  
Hydrate Complex ◽  
Dynamical Properties

The comparison of two different combined quantum mechanical (QM)/molecular mechanical (MM) simulations treating the quantum mechanical region at Hartree-Fock (HF) and B3-LYP density functional theory (DFT) level allowed us to determine structural and dynamical properties of the hydrated calcium ion. The structure is discussed in terms of radial distribution functions, coordination number distributions, and various angular distributions and the dynamical properties, as librations and vibrations, reorientational times and mean residence times were evaluated by means of velocity autocorrelation functions. The QM/MM molecular dynamics (MD) simulation results prove an eightfold-coordinated complex to be the dominant species, yielding average coordination numbers of 7.9 in the HF and 8.0 in the DFT case. Structural and dynamical results show higher rigidity of the hydrate complex using DFT. The high instability of calcium ion's hydration shell allows the observation of water-exchange processes between first and second hydration shell and shows that the mean lifetimes of water molecules in this first shell (<100 ps) have been strongly overestimated by conclusions from experimental data.

Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations

2015 ◽  
Vol 119 (27) ◽  
pp. 8475-8479 ◽  
Author(s):  
Elena García-Giménez ◽  
Antonio Alcaraz ◽  
Marcel Aguilella-Arzo ◽  
Vicente M. Aguilella
Keyword(s):  
Ion Channels ◽  
Analytical Solutions ◽  
Md Simulations ◽  
Numerical Calculations

Binding of bivalent metal cations by α-l-guluronate: insights from the DFT-MD simulations

2015 ◽  
Vol 39 (5) ◽  
pp. 3987-3994 ◽  
Author(s):  
Wojciech Plazinski ◽  
Mateusz Drach
Keyword(s):  
Free Energy ◽  
Metal Ion ◽  
Md Simulations ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Bivalent Metal ◽  
Energy Profiles ◽  
Molecular Aspects ◽  
Insight Into ◽  
Free Energy Profiles

Theoretically calculated free energy profiles give insight into the molecular aspects of metal ion binding by uronate biopolymers.

Hydration Structure and Shear Viscosity of Water Nanoconfined Between Mica Surfaces

2006 ◽  
Author(s):  
Yongsheng Leng ◽  
Peter T. Cummings
Keyword(s):  
Molecular Dynamics ◽  
Liquid Phase ◽  
Shear Rate ◽  
Shear Viscosity ◽  
Surface Force ◽  
Md Simulations ◽  
Force Balance ◽  
Density Distributions ◽  
Wide Range ◽  
Hydration Layers

Molecular dynamics (MD) simulations have been performed to investigate the structure, shear viscosity and dynamics of hydration layers of the thickness of D = 0.61 ∼ 2.44 nm confined between two mica surfaces. For D = 0.92 ∼ 2.44 nm films, water O density distributions indicate that the hydration layers are in liquid phase. The corresponding shear responses are fluidic and similar to those observed in surface force balance (SFB) experiment. However, further increase in confinement leads to the formation of a bilayer ice (D = 0.61 nm) which shows significant shear enhancement and shear thinning over a wide range of shear rate in MD regime, consistent with recent experimental results by shear resonant apparatus for the two mica surfaces in registry.

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