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.

Structure of Water Saturated CTMA-Montmorillonite Hybrid: Molecular Dynamics Simulation Investigation

2011 ◽  
Vol 233-235 ◽  
pp. 1872-1877 ◽  
Author(s):  
Run Liang Zhu ◽  
Thomas V. Shapley ◽  
Marco Molinari ◽  
Ge Fei ◽  
Stephen C. Parker
Keyword(s):  
Molecular Dynamics ◽  
Interlayer Space ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Basal Spacing ◽  
Water Molecules ◽  
Surface Oxygen ◽  
Hydrogen Atoms ◽  
Structure Of Water ◽  
Water Saturated

Molecular dynamics (MD) simulations have been used to investigate the interlayer structure of water saturated organoclays. The basal spacing values of cetyltrimethylammonium (CTMA) intercalated montmorillonite (CTMA-Mont) in dry and water saturated states were detected using XRD. Then the results were compared with simulation results of dry CTMA-Mont. The MD simulations show that the CTMA cations form layer structures on siloxane surface and aggregate in the interlayer space. Water molecules can access part of the siloxane surface and form H-bonds with surface oxygen atoms by donating one or two of the hydrogen atoms. Thus, the water molecules close to the surface have a preferred orientation with the dipole pointing towards the surface, while in the interlayer space, the water molecules aggregate to form large clusters. The H-bonds between surface oxygen and water molecules are shown to be slightly weaker than those between water molecules. Although water molecules within interlayer space can form strong H-bonds as in bulk water the number of H-bond for each water molecule is reduced. Our results indicate that MD simulations represent a useful tool for exploring the microstructure of water saturated organoclays.

A Molecular Dynamics Simulation Study Towards Understanding the Effects of Diameter and Chirality on Hydrogen Adsorption in Singlewalled Carbon Nanotubes

2003 ◽  
Vol 801 ◽  
Author(s):  
Hansong Cheng ◽  
Alan C. Cooper ◽  
Guido P. Pez ◽  
Milen K. Kostov ◽  
Milton W. Cole ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Hydrogen Adsorption ◽  
Md Simulations ◽  
Substantial Effect ◽  
Dynamics Simulation ◽  
Physical Parameters ◽  
Wide Range ◽  
Field Methodology ◽  
Molecular Forces

ABSTRACTA force field methodology has been developed for the description of carbon-carbon and carbon-molecular hydrogen interactions that is ideally suited to modeling hydrogen adsorption on single-walled carbon nanotubes (SWNT). The method makes use of existing parameters of potential functions developed for sp2 and sp3 hybridized carbon atoms and allows accurate representation of molecular forces on curved carbon surfaces. This approach has been used in molecular dynamics (MD) simulations for hydrogen adsorption in SWNT. The results reveal significant nanotube deformations, consistent with ab initio MD simulations, and the calculated energies of adsorption at room temperature are comparable to the reported experimental heats of adsorption for H2 in SWNT. The efficiency of this new method has permitted the MD simulation of hydrogen adsorption on a wide range of SWNT types, varying such parameters as nanotube diameter and chirality. The results show that these SWNT physical parameters have a substantial effect on the energies of adsorption and hydrogen capacities.

Molecular dynamics simulation on the interfacial features of supercritical 1-butene/subcritical water

2014 ◽  
Vol 13 (08) ◽  
pp. 1450066 ◽  
Author(s):  
Huidong Zheng ◽  
Jingjing Chen ◽  
Fangdi Wu ◽  
Suying Zhao
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Subcritical Water ◽  
Md Simulations ◽  
Extraction Process ◽  
Supercritical Condition ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Butanol Concentration ◽  
Subcritical Condition

We studied the interfacial features of 1-butene/water and extraction process of 2-butanol by molecular dynamics (MD) simulations. The infinite dilute diffusion coefficients of 1-butene in water is larger than that of 2-butanol, and one important reason is that 2-butanol molecules can form hydrogen bonds with water molecules. 1-butene is more soluble in water under supercritical condition than that under subcritical condition. 1-butene under supercritical condition can extract more 2-butanol from aqueous solution than that under other conditions. A process of producing 2-butanol by the direct hydration of 1-butene is more competive when it operates under the supercritical conditions of 1-butene which due to a higher solubility of 1-butene in water, a larger diffusion coefficient of 1-butene and a lower 2-butanol concentration in water.

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.

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 Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Krystel El Hage ◽  
Florent Hédin ◽  
Prashant K Gupta ◽  
Markus Meuwly ◽  
Martin Karplus
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Effect ◽  
Md Simulations ◽  
Water Molecules ◽  
Human Hemoglobin ◽  
Standard Size ◽  
Wide Range ◽  
Dynamics Simulations

Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T0) and liganded (R4) tetramers are stable in solution, the published MD simulations of T0 undergo a rapid quaternary transition to an R-like structure. We show that T0 is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T0 tetramer, to be manifested. Even in the largest box, T0 is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.

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.

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 Understanding Covalent Grafting of Nanotubes onto Polymer Nanocomposites: Molecular Dynamics Simulation Study

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2621
Author(s):  
Seunghwa Yang
Keyword(s):  
Molecular Dynamics ◽  
Load Transfer ◽  
Cell Model ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Covalent Grafting ◽  
Modelling Strategies ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes ◽  
External Loads

Here, we systematically interrogate the effects of grafting single-walled (SWNT) and multi-walled carbon nanotubes (MWNT) to polymer matrices by using molecular dynamics (MD) simulations. We specifically investigate key material properties that include interfacial load transfer, alteration of nanotube properties, and dispersion of nanotubes in the polymer matrix. Simulations are conducted on a periodic unit cell model of the nanocomposite with a straight carbon nanotube and an amorphous polyethylene terephthalate (PET) matrix. For each type of nanotube, either 0%, 1.55%, or 3.1% of the carbon atoms in the outermost nanotubes are covalently grafted onto the carbon atoms of the PET matrix. Stress-strain curves and the elastic moduli of nanotubes and nanocomposites are determined based on the density of covalent grafting. Covalent grafting promotes two rivalling effects with respect to altering nanotube properties, and improvements in interfacial load transfer in the nanocomposites are clearly observed. The enhanced interface enables external loads applied to the nanocomposites to be efficiently transferred to the grafted nanotubes. Covalent functionalization of the nanotube surface with PET molecules can alter the solubility of nanotubes and improve dispersibility. Finally, we discuss the current limitations and challenges in using molecular modelling strategies to accurately predict properties on the nanotube and polymers systems studied here.

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

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