Water dynamics in hydrated amorphous materials: a molecular dynamics study of the effects of dehydration in amorphous calcium carbonate

2017 ◽  
Vol 19 (43) ◽  
pp. 29594-29600 ◽  
Author(s):  
Moumita Saharay ◽  
R. James Kirkpatrick
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Amorphous Materials ◽  
Water Dynamics ◽  
Water Molecules ◽  
Transient Phase ◽  
Amorphous Calcium Carbonate

Amorphous calcium carbonate (ACC) is a critical transient phase in the formation of crystalline CaCO3via dehydration of hydrated ACC. Although majority of water molecules in ACC are dynamically restricted, a very small fraction of them (∼2%) shows high diffusivity.

Effects of Magnesium Ions and Water Molecules on the Structure of Amorphous Calcium Carbonate: A Molecular Dynamics Study

2013 ◽  
Vol 117 (47) ◽  
pp. 14849-14856 ◽  
Author(s):  
Hidekazu Tomono ◽  
Hiroki Nada ◽  
Fangjie Zhu ◽  
Takeshi Sakamoto ◽  
Tatsuya Nishimura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Water Molecules ◽  
Magnesium Ions ◽  
Amorphous Calcium Carbonate

scholarly journals Role of Internal Stress in the Early-Stage Nucleation of Amorphous Calcium Carbonate Gels

2020 ◽  
Vol 10 (12) ◽  
pp. 4359 ◽  
Author(s):  
Qi Zhou ◽  
Tao Du ◽  
Lijie Guo ◽  
Gaurav Sant ◽  
Mathieu Bauchy
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Driving Force ◽  
Early Stage ◽  
Local Stress ◽  
Amorphous Calcium Carbonate ◽  
Local Coordination ◽  
Dynamics Simulations ◽  
Over Time

Although calcium carbonate (CaCO3) precipitation plays an important role in nature, its mechanism remains only partially understood. Further understanding the atomic driving force behind the CaCO3 precipitation could be key to facilitate the capture, immobilization, and utilization of CO2 by mineralization. Here, based on molecular dynamics simulations, we investigate the mechanism of the early-stage nucleation of an amorphous calcium carbonate gel. We show that the gelation reaction manifests itself by the formation of some calcium carbonate clusters that grow over time. Interestingly, we demonstrate that the gelation reaction is driven by the existence of some competing local molecular stresses within the Ca and C precursors, which progressively get released upon gelation. This internal molecular stress is found to originate from the significantly different local coordination environments exhibited by Ca and C atoms. These results highlight the key role played by the local stress acting within the atomic network in governing gelation reactions.

scholarly journals Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase

Biomolecules ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1664
Author(s):  
Sofya V. Lushchekina ◽  
Gaetan Inidjel ◽  
Nicolas Martinez ◽  
Patrick Masson ◽  
Marie Trovaslet-Leroy ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Sucrose Concentration ◽  
Water Dynamics ◽  
Water Molecules ◽  
Protein Surface ◽  
Incoherent Neutron Scattering ◽  
Enzyme Model ◽  
Non Linear ◽  
Model Mouse ◽  
Dynamics Simulations

The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.

Structure and Transformation of Amorphous Calcium Carbonate: A Solid-State 43Ca NMR and Computational Molecular Dynamics Investigation

2012 ◽  
Vol 24 (10) ◽  
pp. 1828-1836 ◽  
Author(s):  
Jared Wesley Singer ◽  
A. Özgür Yazaydin ◽  
R. James Kirkpatrick ◽  
Geoffrey M. Bowers
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Solid State ◽  
Amorphous Calcium Carbonate

Molecular Dynamics Simulation of Water and Ions in Nanopores of Lysozyme Protein Crystal

2011 ◽  
Vol 9 (1) ◽  
Author(s):  
Nafiseh Farhadian ◽  
Mojtaba Shariaty-niassar ◽  
Kourosh Malek ◽  
Ali Maghari
Keyword(s):  
Molecular Dynamics ◽  
Water Dynamics ◽  
Dynamics Simulation ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Water Molecules ◽  
Surface Zone ◽  
Hydration Layer ◽  
Core Zone ◽  
Diffusion Behavior

Highly porous cross-linked protein crystals are a novel class of nanoporous materials with vast applications in biocatalysis and selective separation membranes. Long time equilibrium molecular dynamics (MD) simulations were performed to study the behavior of water and ions in the nanopores of lysozyme protein crystals. Pore size profile along different axes showed that the main pores lie along the z-axis consisting of an anisotropic structure. The morphology of pore network and pore sizes, influence water dynamics in protein crystals. Transport properties of water molecules were investigated under two diffusion regimes around protein surface, i.e. surface and core zone. Results showed that water molecules near the surface zone had the anomalous diffusion behavior while the behavior in the core zone was diffusive. Moreover, an anisotropic diffusion behavior was occurred along different axes in accordance to experimental predictions. Simulations demonstrated that nearly 16 percent of water molecules have the residence time above 100 ps at the first hydration layer around the protein crystal, while 3.3 percent of those remain in the cavities over a longer time of about 1400 ps. The behavior of chloride counter ions in the first hydration layer around the protein crystal or on the specific residues of the crystal was investigated as well. The simulation results were in a good agreement with the previous theoretical studies and experimental data. This study provides valuable insights into understanding the transport phenomena in the protein crystals in view of the nature of solvent-protein and ion-protein interactions.

scholarly journals How does an amorphous surface influence molecular binding? – ovocleidin-17 and amorphous calcium carbonate

2015 ◽  
Vol 17 (26) ◽  
pp. 17494-17500 ◽  
Author(s):  
Colin L. Freeman ◽  
John H. Harding ◽  
David Quigley ◽  
P. Mark Rodger
Keyword(s):  
Molecular Dynamics ◽  
Calcium Carbonate ◽  
Molecular Dynamics Simulations ◽  
Amorphous Calcium Carbonate ◽  
Molecular Binding ◽  
Dynamics Simulations ◽  
Amorphous Surface

Molecular dynamics simulations of the protein ovocleidin-17 binding to the surface of amorphous calcium carbonate highlighting the residues contacting the surface.

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 Molecular dynamics simulation of protein-mediated biomineralization of amorphous calcium carbonate

RSC Advances ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 1653-1663 ◽  
Author(s):  
R. Sandya Rani ◽  
Moumita Saharay
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Calcium Carbonate ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Amorphous Calcium Carbonate ◽  
Charged Amino Acids ◽  
Living Organisms

The protein-mediated biomineralization of calcium carbonate (CaCO3) in living organisms is primarily governed by critical interactions between the charged amino acids of the protein, solvent, calcium (Ca2+) and carbonate (CO32−) ions.

Anhydrous amorphous calcium carbonate (ACC) is structurally different from the transient phase of biogenic ACC

2019 ◽  
Vol 55 (48) ◽  
pp. 6946-6949 ◽  
Author(s):  
Chieh Tsao ◽  
Pao-Tao Yu ◽  
Chin-Hsuan Lo ◽  
Chung-Kai Chang ◽  
Chia-Hsin Wang ◽  
...  
Keyword(s):  
Heat Treatment ◽  
Phase Transformation ◽  
Water Vapor ◽  
Calcium Carbonate ◽  
Pressure Range ◽  
Ambient Pressure ◽  
Transient Phase ◽  
Amorphous Calcium Carbonate ◽  
X Ray

An in situ ambient pressure soft X-ray spectroscopic study of the phase transformation of ACC exposed to water vapor in the mbar pressure range in conjunction with heat treatment.

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