Molecular Dynamics of Cation Hydration in the Presence of Carboxylated Molecules: Implications for Calcification

2011 ◽  
Vol 1301 ◽  
Author(s):  
Laura M. Hamm ◽  
Adam F. Wallace ◽  
Patricia M. Dove
Keyword(s):  
Molecular Dynamics ◽  
Divalent Cations ◽  
Bulk Water ◽  
Ion Pair ◽  
Water Molecules ◽  
Residence Times ◽  
Polymorph Selection ◽  
Inner Sphere ◽  
Cation Hydration ◽  
Kinetics Of

ABSTRACTBiomolecules rich in aspartic acid (Asp) are known to play a role in biomineral morphology and polymorph selection, and have been shown to greatly enhance the growth kinetics of calcite. The mechanism by which these compounds favor calcification may be related to their effects upon cation solvation. Using molecular dynamics, we investigated the influence of small carboxylated molecules on the hydration states and water exchange rates of divalent cations. We show that the carboxylate moieties of Asp promote dehydration of Ca2+ and Sr2+ and that contact ion pair (CIP) formation is not required to disrupt the hydration of these cations. Ca2+- Asp and Sr2+ - Asp CIP formation decreases the total inner sphere coordination from an average of 8.0 and 8.4 in bulk water to 7.5 and 8.0, respectively. Water residence times estimated for Mg2+, Ca2+and Sr2+ follow the expected trend of decreasing residence time with increasing ionic radius. In the presence of Asp, both solvent-separated ion pair (SSIP) and CIP formation decrease the residence times of Ca2+and Sr2+ inner sphere water molecules. Comparable impacts on Mg2+ hydration are not observed. Mg2+ - Asp CIP formation is energetically unfavorable and Asp does not affect Mg2+ inner sphere water residence times.

Molecular Dynamics Simulation of Water Transporting Through Nanotube Driven by Concentration Difference

2011 ◽  
Author(s):  
Ning Zhang ◽  
Weizhong Li ◽  
Jing Cui
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Flow Behavior ◽  
Bulk Water ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Flowing Water ◽  
Water Density ◽  
Concentration Difference ◽  
Water Chain

A flowing water chain in a (6, 6) carbon nanotube (CNT) driven by concentration difference is studied by molecular dynamics (MD) simulation. Water molecules in the CNT form a continuous water chain, which occupy the space of a 2 Å radius along the axis of channel. By computing the trajactory from the simulation run, the water density profile along the CNT is obtained and the flow behavior of water in the CNT is studied. The simulated results show that the density distribution in the CNT is lower than that in the bulk water and the solution, but the free energy distribution appears a contrary tendency. In addition, the quantity of hydrogen-bonds (H-bonds) forming in the CNT appears a fluctuation along with time, by analyzing which, it is found that the formation of H-bonds in the CNT is related to flow rate of water.

scholarly journals Effect of Size and Temperature on Water Dynamics inside Carbon Nano-Tubes Studied by Molecular Dynamics Simulation

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6175
Author(s):  
Amit Srivastava ◽  
Jamal Hassan ◽  
Dirar Homouz
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Underlying Mechanism ◽  
Bulk Water ◽  
Water Dynamics ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Wide Range ◽  
Carbon Nano Tubes ◽  
20 Nm

Water transport inside carbon nano-tubes (CNTs) has attracted considerable attention due to its nano-fluidic properties, its importance in nonporous systems, and the wide range of applications in membrane desalination and biological medicine. Recent studies show an enhancement of water diffusion inside nano-channels depending on the size of the nano-confinement. However, the underlying mechanism of this enhancement is not well understood yet. In this study, we performed Molecular Dynamics (MD) simulations to study water flow inside CNT systems. The length of CNTs considered in this study is 20 nm, but their diameters vary from 1 to 10 nm. The simulations are conducted at temperatures ranging from 260 K to 320 K. We observe that water molecules are arranged into coaxial water tubular sheets. The number of these tubular sheets depends on the CNT size. Further analysis reveals that the diffusion of water molecules along the CNT axis deviates from the Arrhenius temperature dependence. The non-Arrhenius relationship results from a fragile liquid-like water component persisting at low temperatures with fragility higher than that of the bulk water.

scholarly journals Recognition of N6-methyladenosine by the YTHDC1 YTH domain studied by molecular dynamics and NMR spectroscopy: The role of hydration

2021 ◽  
Author(s):  
Miroslav Krepl ◽  
Fred Franz Damberger ◽  
Christine von Schroetter ◽  
Dominik Theler ◽  
Pavlína Pokorná ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Binding Pocket ◽  
Bulk Water ◽  
Titration Calorimetry ◽  
Water Molecules ◽  
Water Network ◽  
Solvent Interactions ◽  
Yth Domain ◽  
The Cost

AbstractBackgroundThe YTH domain of YTHDC1 belongs to a class of protein “readers”, recognizing the N6-methyladenosine (m6A) chemical modification in mRNA. Static ensemble-averaged structures revealed details of N6-methyl recognition via a conserved aromatic cage.MethodsWe performed molecular dynamics (MD) simulations along with nuclear magnetic resonance (NMR) and isothermal titration calorimetry (ITC) measurements to examine how dynamics and solvent interactions contribute to the m6A recognition and negative selectivity towards unmethylated substrate.ResultsAn intricate network of water-mediated interactions surrounds bound m6A. The unmethylated adenosine allows disruptive intrusions of bulk water deep into the binding pocket, increasing selectivity for m6A. We furthermore show that the YTHDC1’s preference for the 5′-Gm6A-3′ motif is partially facilitated by a network of water-mediated interactions between the 2-amino group of the preceding guanosine and residues deep in the m6A binding pocket. The 5′-Im6A-3′ (where I is inosine) motif can be recognized as well at the cost of disrupting the water network and a small decrease in affinity. The YTHDC1 D479A mutant, which interrupts the water network, also destabilizes m6A binding. Lastly, we formulate and test an easy-to-implement approach for increasing the agreement between simulations and NMR experiments by using the HBfix potential function for stabilization of key NOE distances. We call the new approach NOEfix.ConclusionsThe structured water molecules surrounding the bound RNA and the methylated substrate’s ability to exclude bulk water molecules are important elements of the YTH domain’s preference for m6A. Network of water molecules also fine tunes the specificity towards 5′-Gm6A-3′ motifs.General SignificanceOur interdisciplinary study of YTHDC1 protein/RNA complex reveals an unusual mechanism by which solvent dynamics can contribute towards recognition of methylation by proteins.

Molecular Dynamics Investigation of Water Behavior Through Nanopores

2020 ◽  
Author(s):  
Kimia Montazeri ◽  
Penghui Cao ◽  
Yoonjin Won
Keyword(s):  
Molecular Dynamics ◽  
Bulk Water ◽  
Energy Storage And Conversion ◽  
Water Molecules ◽  
Transport Mechanisms ◽  
Confined Water ◽  
Nanoscale Transport ◽  
Wetting Properties ◽  
Velocity Autocorrelation ◽  
Water Behavior

Abstract The transport of fluids through nanoscale pores, channels, and membranes has been of great importance in our daily life. Nanoscale transport is relevant to many applications such as agriculture, energy and environmental fields. Considering these applications, it is important to characterize detailed mechanisms of liquid transport through nanoscale defects and pores on surfaces. Such characterization requires a detailed understanding of the deviation of water behavior and its transport mechanisms in nanoscale from bulk water. Molecular dynamics provide proper means to understand the dynamics and mechanisms of motions of water molecules confined in ultra-small spaces. This work examines the water transport through an individual pore which has a nanoscale dimensions ranging from 1.0 to 1.8 nm from molecular dynamics perspective. The effects of the nanopore dimensions as well as the surface wetting properties on the behavior of confined water are studied. The translational and rotational dynamics of water molecules are characterized by examining velocity autocorrelation functions and the calculation of the density of states, which supports the presence of unusual, solid-like behaviors of water molecules. A good understanding of the transport mechanisms and their origins are crucial to address common challenges in many engineering applications such as energy storage and conversion and could pave the way towards more efficient water-energy systems.

Long-range Structures in Bulk Water. A Molecular Dynamics Study

1997 ◽  
Vol 52 (5) ◽  
pp. 432-434 ◽  
Author(s):  
Axel Kohlmeyer ◽  
Wolfgang Witschel ◽  
Eckhard Spohr
Keyword(s):  
Molecular Dynamics ◽  
Correlation Functions ◽  
Pair Correlation ◽  
Bulk Water ◽  
Water Molecules ◽  
Partial Structure ◽  
Pair Correlation Functions ◽  
Large Bulk ◽  
Structure Factors ◽  
Dynamics Simulations

Abstract We present recent calculations of pair correlation functions and partial structure factors derived from molecular dynamics simulations of large bulk water systems (up to 12 167 water molecules). We observe small amplitude oscillations of the pair correlation functions in the range between 10 and 20 Ä.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

scholarly journals The Impact of the Electric Field on Surface Condensation of Water Vapor: Insight from Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 64 ◽  
Author(s):  
Qin Wang ◽  
Hui Xie ◽  
Zhiming Hu ◽  
Chao Liu
Keyword(s):  
Molecular Dynamics ◽  
Water Vapor ◽  
Electric Field ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Attraction Force ◽  
Condensation Rate ◽  
Shape Transformation ◽  
The Impact

In this study, molecular dynamics simulations were carried out to study the coupling effect of electric field strength and surface wettability on the condensation process of water vapor. Our results show that an electric field can rotate water molecules upward and restrict condensation. Formed clusters are stretched to become columns above the threshold strength of the field, causing the condensation rate to drop quickly. The enhancement of surface attraction force boosts the rearrangement of water molecules adjacent to the surface and exaggerates the threshold value for shape transformation. In addition, the contact area between clusters and the surface increases with increasing amounts of surface attraction force, which raises the condensation efficiency. Thus, the condensation rate of water vapor on a surface under an electric field is determined by competition between intermolecular forces from the electric field and the surface.

scholarly journals Electrical Breakdown Mechanism of Transformer Oil with Water Impurity: Molecular Dynamics Simulations and First-Principles Calculations

Crystals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 123
Author(s):  
Bin Cao ◽  
Ji-Wei Dong ◽  
Ming-He Chi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Diffusion ◽  
First Principles ◽  
Electrical Breakdown ◽  
Transformer Oil ◽  
Water Molecules ◽  
Conducting Channel ◽  
Breakdown Mechanism ◽  
Water Impurity ◽  
Dynamics Simulations

Water impurity is the essential factor of reducing the insulation performance of transformer oil, which directly determines the operating safety and life of a transformer. Molecular dynamics simulations and first-principles electronic-structure calculations are employed to study the diffusion behavior of water molecules and the electrical breakdown mechanism of transformer oil containing water impurities. The molecular dynamics of an oil-water micro-system model demonstrates that the increase of aging acid concentration will exponentially expedite thermal diffusion of water molecules. Density of states (DOS) for a local region model of transformer oil containing water molecules indicates that water molecules can introduce unoccupied localized electron-states with energy levels close to the conduction band minimum of transformer oil, which makes water molecules capable of capturing electrons and transforming them into water ions during thermal diffusion. Subsequently, under a high electric field, water ions collide and impact on oil molecules to break the molecular chain of transformer oil, engendering carbonized components that introduce a conduction electronic-band in the band-gap of oil molecules as a manifestation of forming a conductive region in transformer oil. The conduction channel composed of carbonized components will be eventually formed, connecting two electrodes, with the carbonized components developing rapidly under the impact of water ions, based on which a large number of electron carriers will be produced similar to “avalanche” discharge, leading to an electrical breakdown of transformer oil insulation. The water impurity in oil, as the key factor for forming the carbonized conducting channel, initiates the electric breakdown process of transformer oil, which is dominated by thermal diffusion of water molecules. The increase of aging acid concentration will significantly promote the thermal diffusion of water impurities and the formation of an initial conducting channel, accounting for the degradation in dielectric strength of insulating oil containing water impurities after long-term operation of the transformer.

scholarly journals Morphology, energetics and growth kinetics of diphenylalanine fibres

2021 ◽  
Author(s):  
Phillip Mark Rodger ◽  
Caroline Montgomery ◽  
Giovanni Costantini ◽  
Alison Rodger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Growth Kinetics ◽  
Dynamics Simulations ◽  
Kinetics Of

The formation and stability of diphenylalanine fibres are studied by combining molecular dynamics simulations with microscopy and spectroscopy experiments, quantitatively detailing their morphology, energetics and growth kinetics.

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