scholarly journals Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field

2021 ◽  
Vol 155 (8) ◽  
pp. 084503
Author(s):  
Sebastian Falkner ◽  
Nadine Schwierz
Keyword(s):  
Force Field ◽  
Water Exchange ◽  
Hydration Shell ◽  
Water Model ◽  
Ionic Force ◽  
Influence Of Water ◽  
First Hydration Shell

scholarly journals Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field

2021 ◽  
Author(s):  
Sebastian Falkner ◽  
Nadine Schwierz
Keyword(s):  
Force Field ◽  
Water Exchange ◽  
Force Fields ◽  
Hydration Shell ◽  
Water Model ◽  
Polarizable Force Fields ◽  
Ionic Force ◽  
Influence Of Water ◽  
Biomolecular Simulations ◽  
Dynamics Simulations

Water exchange between the first and second hydration shell is essential for the role of Mg2+ in biochemical processes. In order to provide microscopic insights into the exchange mechanism, we resolve the exchange pathways by all-atom molecular dynamics simulations and transition path sampling. Since the exchange kinetics relies on the choice of the water model and the ionic force field, we systematically investigate the influence of seven different polarizable and non-polarizable water and three different Mg2+ models. In all cases, water exchange can occur either via an indirect or direct mechanism (exchanging molecules occupy different/same position on water octahedron). In addition, the results reveal a crossover from an interchange dissociative (Id) to an associative (Ia) reaction mechanism dependent on the range of the Mg2+-water interaction potential of the respective force field. Standard non-polarizable force fields follow the Id mechanism in agreement with experimental results. By contrast, polarizable and long-ranged non-polarizable force fields follow the Ia mechanism. Our results provide a comprehensive view on the influence of the water model and ionic force field on the exchange dynamics and the foundation to assess the choice of the force field in biomolecular simulations.

A Molecular Dynamics Study of the Structure of an Aqueous CsF Solution

1983 ◽  
Vol 38 (2) ◽  
pp. 214-224 ◽  
Author(s):  
Gy. I. Szász ◽  
K. Heinzinger
Keyword(s):  
Molecular Dynamics ◽  
Hydration Shell ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Water Model ◽  
Water Molecules ◽  
Heat Of Solution ◽  
Average Temperature ◽  
Experimental Density ◽  
First Hydration Shell

Abstract A molecular dynamics simulation of a 2.2 molal aqueous CsF solution has been performed employing the ST2 water model. The basic periodic cube with a sidelength of 18.50 Å contained 200 water molecules, and 8 ions of each kind, corresponding to an experimental density of 1.26 g/cm3. The simulation extended over 6.5 ps with an average temperature of 307 K. The structure of the solution is discussed by means of radial distribution functions and the orientation of the water molecules. The computed hydration numbers in the first shell of Cs+ and F- are 7.9 and 6.8, respectively; the corresponding first hydration shell radii are 3.22 A and 2.64 A, respectively. Values for the hydration shell energies and the heat of solution have been calculated.

scholarly journals Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E

2021 ◽  
Author(s):  
Kara K. Grotz ◽  
Nadine Schwierz
Keyword(s):  
Force Field ◽  
Water Exchange ◽  
Optimal Parameter ◽  
Hydration Shell ◽  
Vital Role ◽  
Ion Binding ◽  
Enhanced Sampling ◽  
Water Models ◽  
Force Field Parameters ◽  
Dynamics Simulations

Magnesium plays a vital role in a large variety of biological processes. To model such processes by molecular dynamics simulations, researchers rely on accurate force field parameters for Mg2+ and water. OPC is one of the most promising water models yielding an improved description of biomolecules in water. The aim of this work is to provide force field parameters for Mg2+ that lead to accurate simulation results in combination with OPC water. Using twelve different Mg2+ parameter sets, that were previously optimized with different water models, we systematically assess the transferability to OPC based on a large variety of experimental properties. The results show that the Mg2+ parameters for SPC/E are transferable to OPC and closely reproduce the experimental solvation free energy, radius of the first hydration shell, coordination number, activity derivative, and binding affinity toward the phosphate oxygen on RNA. Two optimal parameter sets are presented: MicroMg yields water exchange in OPC on the microsecond timescale in agreement with experiments. NanoMg yields accelerated exchange on the nanosecond timescale and facilitates the direct observation of ion binding events for enhanced sampling purposes.

Ab initio investigation of the first hydration shell of glucose

2020 ◽  
Vol 496 ◽  
pp. 108114
Author(s):  
Ran Song ◽  
Dong Chen ◽  
Chengxiang Suo ◽  
Zhiheng Guo
Keyword(s):  
Ab Initio ◽  
Hydration Shell ◽  
First Hydration Shell

scholarly journals Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations

2020 ◽  
Author(s):  
Anshuman Kumar ◽  
Siobhan E. Toal ◽  
David DiGuiseppi ◽  
Reinhard Schweitzer-Stenner ◽  
Bryan Wong
Keyword(s):  
Circular Dichroism ◽  
Absorption Spectra ◽  
Density Functional ◽  
Time Dependent ◽  
Water Model ◽  
Cd Spectra ◽  
Influence Of Water ◽  
Explicit Consideration ◽  
A Charge ◽  
Circular Dichroïsm

<p>We investigate the UV absorption spectra of a series of cationic GxG (where x denotes a guest residue) peptides in aqueous solution and find that the spectra of a subset of peptides with x = A, L, I, K, N, and R (and, to a lesser extent, peptides with x = D and V) vary as a function of temperature. To explore whether or not this observation reflects conformational dependencies, we carry out time-dependent density functional calculations for the polyproline II (pPII) and β-strand conformations of a limited set of tripeptides (x = A, V, I, L, and R) in implicit and explicit water. We find that the calculated CD spectra for pPII can qualitatively account for the experimental spectra irrespective of the water model. The reproduction of the <i>β</i>-strand UV-CD spectra, however, requires the explicit consideration of water. Based on the calculated absorption spectra, we explain the observed temperature dependence of the experimental spectra as being caused by a reduced dispersion (larger spectral density) of the overlapping NV<sub>2</sub> band and the influence of water on electronic transitions in the β-strand conformation. Contrary to conventional wisdom, we find that both the NV<sub>1</sub> and NV<sub>2</sub> band are the envelopes of contributions from multiple transitions that involve more than just the HOMOs and LUMOs of the peptide groups. A natural transition orbital analysis reveals that some of the transitions with significant oscillator strength have a charge-transfer character. The overall manifold of transitions, in conjunction with their strengths and characters, depends on the peptide’s backbone conformation, peptide hydration, and also on the side chain of the guest residue. It is particularly noteworthy that molecular orbitals of water contribute significantly to transitions in <i>β</i>-strand conformations. Our results reveal that peptide groups, side chains, and hydration shells must be considered as an entity for a physically valid characterization of UV absorbance and circular dichroism. </p>

On the size, shape and energetics of the hydration shell around alkanes

2021 ◽  
Author(s):  
Giuseppe Lanza ◽  
Maria Assunta Chiacchio
Keyword(s):  
Hydration Shell ◽  
Clathrate Hydrates ◽  
First Hydration Shell

A large breath of clathrate-like cages has been proposed as the very first hydration shell of alkanes. The cages include canonical structures commonly found in clathrate hydrates and many others,...

scholarly journals Evaluation and Improvement of the Amber ff99SB Force Field with an Advanced Water Model

2011 ◽  
Vol 100 (3) ◽  
pp. 311a
Author(s):  
Paul S. Nerenberg ◽  
Clare So ◽  
Ajay Tripathy ◽  
Teresa Head-Gordon
Keyword(s):  
Force Field ◽  
Water Model

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field
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