scholarly journals Bridging the 12-6-4 Model and the Fluctuating Charge Model

2021 ◽  
Vol 9 ◽  
Author(s):  
Pengfei Li
Keyword(s):  
Metal Ions ◽  
Biological Systems ◽  
Md Simulations ◽  
Dipole Interaction ◽  
Solvation Shell ◽  
Water Molecules ◽  
Atomic Charges ◽  
Induced Dipole ◽  
Charge Model ◽  
Simulation Results

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r4 based on theory. Hence, we developed the 12-6-4 model and showed it could solve this deficiency in a physically meaningful way. However, our previous research also found that the 12-6-4 model overestimated the coordination numbers (CNs) for some highly charged metal ions. And we attributed this artifact to that the current 12-6-4 scheme lacks a correction for the interactions among the first solvation shell water molecules. In the present study, we considered the ion-included dipole interaction by using the 12-6 model with adjusting the atomic charges of the first solvation shell water molecules. This strategy not only considers the ion-induced dipole interaction between ion and the first solvation shell water molecules but also well accounts for the increased repulsion among these water molecules compared to the bulk water molecules. We showed this strategy could well reproduce the experimental HFE and IOD values for Mg2+, Zn2+, Al3+, Fe3+, and In3+ and solve the CN overestimation issue of the 12-6-4 model for Fe3+ and In3+. Moreover, our simulation results showed good agreement with previous ab initio MD simulations. In addition, we derived the physical relationship between the C4 parameter and induced dipole moment, which agreed well with our simulation results. Finally, we discussed the implications of the present work for simulating metalloproteins. Due to the fluctuating charge model uses a similar concept to the 12-6 model with adjusting atomic charges, we believe the present study builds a bridge between the 12-6-4 model and the fluctuating charge model.

Boosting Performance by Water Solvation Shell with Hydrogen Bonds on Protonic Ionic Liquid: Insights into the Acid Catalysis of Glycosidic Bond

2021 ◽  
Author(s):  
Kaixin Li ◽  
Limin Deng ◽  
Shun Yi ◽  
Yabo Wu ◽  
Guangjie Xia ◽  
...  
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Hydrogen Bonds ◽  
Acid Catalysis ◽  
Biological Systems ◽  
Solvation Shell ◽  
Water Molecules ◽  
Binding Behavior ◽  
Chemical And Biological Systems

Hydrogen-bonding (HB) induced by water solvation shell is vital in the chemical and biological systems. Herein, HBs related to the binding behavior of protonic ionic liquids (PIL) with water molecules...

scholarly journals Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies

2012 ◽  
Vol 85 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Thomas J. Penfold ◽  
Christopher J. Milne ◽  
Ivano Tavernelli ◽  
Majed Chergui
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Solvation Shell ◽  
Water Molecules ◽  
Time Resolved ◽  
X Ray ◽  
Bond Network ◽  
Hydrophobic Solvation ◽  
X Ray Absorption ◽  
Small Anisotropy

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes observed upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives for 3–4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell.

Solution chemistry effects on the solvation shell of metal ions

2020 ◽  
Author(s):  
Xiangwen Wang ◽  
Dimitrios Toroz ◽  
Seonmyeong Kim ◽  
Simon Clegg ◽  
Gun-Sik Park ◽  
...  
Keyword(s):  
Metal Ions ◽  
Pure Water ◽  
Solvation Shell ◽  
Solution Chemistry ◽  
Chemical Characteristics ◽  
Velocity Autocorrelation Function ◽  
Ionic Solvation ◽  
General Terms ◽  
Alkaline Earth Metal Ions ◽  
Wide Range

<div> <p>As natural aqueous solutions are far from being pure water, being rich in ions, the properties of solvated ions are of relevance for a wide range of systems, including biological and geochemical environments. We conducted ab initio and classical MD simulations of the alkaline earth metal ions Mg<sup>2+</sup> and Ca<sup>2+</sup> and of the alkali metal ions Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup> and Cs<sup>+</sup> in pure water and electrolyte solutions containing the counterions Cl<sup>–</sup> and SO<sub>4</sub><sup>2–</sup>. Through a detailed analysis of these simulations, this study reports on the effect of solution chemistry (composition and concentration of the solution) to the ion–water structural properties and interaction strength, and to the dynamics, hydrogen bond network, and low-frequency dynamics of the ionic solvation shell. Except for the ion–water radial distribution function, which is weakly dependent on the counter-ions and concentrations, we found that all other properties can be significantly influenced by the chemical characteristics of the solution. Calculation of the velocity autocorrelation function of magnesium ions, for example, shows that chlorine ions located in the second coordination shell of Mg<sup>2+</sup> weaken the Mg(H<sub>2</sub>O)<sub>6</sub><sup>2+</sup> hydration ‘cage’ of the cation. The result reported in this study suggest that ionic solvation shell can be significantly influenced by the interactions between other ions present in solution ions, especially those of opposite charge. In more general terms, the chemical characteristics of the solution, including the balance between ion-solvent and ion-ion interactions, could result in significant differences in behavior and function of the ionic solvation shell.</p> </div>

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy

2018 ◽  
Author(s):  
Daniel R. Moberg ◽  
Shelby C. Straight ◽  
Francesco Paesani
Keyword(s):  
Temperature Dependence ◽  
Low Frequency ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Sum Frequency Generation ◽  
Water Molecules ◽  
Water Interface ◽  
Sum Frequency ◽  
Air Water Interface ◽  
Frequency Generation

<div> <div> <div> <p>The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The total vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular auto-correlation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating 0, 1, or 2 hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm−1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules. </p> </div> </div> </div>

scholarly journals Detection of metal ions in biological systems: A review

2020 ◽  
Vol 39 (1) ◽  
pp. 231-246 ◽  
Author(s):  
Xian Zheng ◽  
Wenyu Cheng ◽  
Chendong Ji ◽  
Jin Zhang ◽  
Meizhen Yin
Keyword(s):  
Metal Ions ◽  
Metal Ion ◽  
Metabolic Regulation ◽  
Organic Dyes ◽  
Biological Systems ◽  
High Sensitivity ◽  
Transportation Energy ◽  
Material Transportation ◽  
High Fluorescence ◽  
Metal Ion Detection

Abstract Metal ions are widely present in biological systems and participate in many critical biochemical processes such as material transportation, energy conversion, information transmission and metabolic regulation, making them indispensable substance in our body. They can cause health problems when deficiency or excess occurs. To understand various metabolic processes and facilitate diseases diagnosis, it is very important to measure the content and monitor the distribution of metal ions in individual cells, tissues and whole organisms. Among the various methods for metal ion detection, fluorescent sensors with organic dyes have attracted tremendous attention due to many advantages such as high fluorescence quantum yield, facile modification approaches and biocompatibility in addition to operation ease, high sensitivity, fast detection speed, and real-time detection. This review summarizes the recent progress on the detection and imaging of the metal ions in biological systems including Na+, K+, Ca2+, Mg2+, Fe2+/Fe3+, Zn2+, and Cu2+ provides an opinion on remaining challenges to be addressed in this field.

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