Structure and Dynamics of Interfacial Water on Muscovite Surface under Different Temperature Conditions (298 K to 673 K): Molecular Dynamics Investigation

We performed molecular dynamics (MD) simulations to study structure, stability, and dynamics of the water adsorption layer on muscovite mica at several temperatures (from 298 K to 673 K) and pressures (0.1 MPa, 10 MPa, and 50 MPa). We studied the structure of the adsorption layers with three characteristic peaks of density and orientation of H2O molecules in one-dimensional and two-dimensional profiles. The results show that the water adsorption layers become less structured and more mobile as the temperature increases. We also found the first and the second layers are less diffusive than the third one, and the difference of diffusivity gets unclear as the temperature increases. Finally, we discuss implications to hydration forces and wettability, which are significant interfacial properties of the multiphase fluids system such as water/gas/mineral systems, from the viewpoint of water adsorption film with nanometer thickness.

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Molecular Simulation of Adsorbed Water on Mesoporous Silica Thin Films

ASME 2013 11th International Conference on Nanochannels, Microchannels, and Minichannels ◽

10.1115/icnmm2013-73131 ◽

2013 ◽

Author(s):

Kyohei Yamashita ◽

Hirofumi Daiguji

Keyword(s):

Thin Films ◽

Mesoporous Silica ◽

Water Adsorption ◽

Pore Radius ◽

Md Simulations ◽

Adsorption Properties ◽

Pore Surface ◽

Silica Thin Films ◽

Adsorption Layers ◽

Kinetics Of

Grand canonical Monte Carlo (GCMC) and canonical ensemble molecular dynamics (NVT-MD) simulations were performed to investigate water adsorption properties in mesoporous silica thin films. The effect of pore radius on the adsorption properties was assessed using two models of mesoporous silica thin films having different pore radius and film thickness (1.38 and 5.66 nm in Model 1, respectively, and 1.81 and 7.30 nm in Model 2, respectively). In the simulations, a water adsorption layer or water menisci were formed in a mesopore accompanying the growth or shrinkage of stable adsorption layers on the upper and lower surfaces. The stable two water adsorption layers were formed on the pore surface in both models. The curvature radius of a water meniscus decreased monotonically and approached a constant value. In addition, NVT-MD simulations were performed to investigate the kinetics of water uptake into a model of mesoporous silica thin film having a radius and thickness of 1.38 and 7.93 nm (Model 3). The calculation results showed that the kinetics of water uptake depended on the number of water molecules and there were two different transport mechanisms in the pore. One was diffusion of water along the pore surface, and the other was capillary rise of liquid water.

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Developing Cross Drag Expressions for Nanotube Bundles Using Molecular Dynamics

ASME 2011 9th International Conference on Nanochannels, Microchannels, and Minichannels, Volume 2 ◽

10.1115/icnmm2011-58045 ◽

2011 ◽

Author(s):

Masoud Darbandi ◽

Rasoul Khaledi-Alidusti ◽

Majid Abbaspour ◽

Hossein Reza Abbasi ◽

Moslem Sabouri ◽

...

Keyword(s):

Molecular Dynamics ◽

Fluid Flows ◽

Md Simulations ◽

Liquid Argon ◽

Nonequilibrium Molecular Dynamics ◽

Empirical Expressions ◽

Macro Scale ◽

Slow Flows ◽

The Cross ◽

The Difference

The nonequilibrium molecular dynamics (NEMD) simulations are performed to calculation the cross drag over a nanotube located in a uniform liquid argon flow. As is known, the behavior of fluid flows in nano-scale sizes is very different from that in microscopic and macroscopic sizes. In this work, our concern is on the flow of argon molecules over a nanotube which occurs in nanoscale sizes. We calculate the cross drag enforced the nanotube at Re≤1.0. In this regard, we use the molecular dynamics and simulate the flow of argon molecules over (6,0), (8,0) and (10,0) nanotubes. The simulations are performed at different velocities and the cross drag coefficient is computed at different Reynolds numbers. To improve the efficiency of simulations, we use USHER algorithm and examin the insertion of molecules at the end of the simulation box, the argon molecules are located out of box. Using the power trend line, we derived a formula, which approximates the cross drag of chosen nanotube. In all simulations, only the first two and the last two rings of the nanotube are frozen. All non-bonded interactions are calculated based on the Lennard-Jones potential. The results if molecular dynamics are compared with two empirical expressions provided by experiments performed on the flow over a macro-scale cylinder. The results show that the cross drag force on a single-walled nanotube calculated from MD simulations is larger than that provided by the empirical expressions in slow flows (Re≪ 1.0). As is expected the results of continuum flow calculations cannot be trusted to predict the drag of a nanotubes if Re≪1.0. The difference increases as the flow velocity decreases.

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Vibration of Cantilevered Double-Walled Carbon Nanotubes Predicted by Timoshenko Beam Model and Molecular Dynamics

International Journal of Computational Methods ◽

10.1142/s0219876215400174 ◽

2015 ◽

Vol 12 (04) ◽

pp. 1540017 ◽

Cited By ~ 8

Author(s):

Rumeng Liu ◽

Lifeng Wang

Keyword(s):

Carbon Nanotubes ◽

Molecular Dynamics ◽

Natural Frequencies ◽

Md Simulations ◽

Beam Model ◽

Timoshenko Beams ◽

Fundamental Frequencies ◽

The Difference ◽

Double Walled Carbon Nanotubes ◽

Walled Carbon Nanotubes

Vibration of double-walled carbon nanotubes (DWCNTs) with one end fixed and the other end free is studied by using different beam models of continuum mechanics and the molecular dynamics (MD) simulations. The models of the double-Euler beams (DEB) and the double-Timoshenko beams (DTB) of cantilevered case, with the van der Waals interaction between layers taken into consideration, are applied to predict the natural frequencies of DWCNTs. An analytical solution is first obtained for the DTB model with cantilevered boundary condition. The fundamental frequencies obtained by the DEB model and the DTB model are very close, for the relatively long DWCNTs. The MD simulations show that these two models can predict the natural frequencies well. However, the difference between the DEB model and the DTB model becomes obvious, for the vibration of the relatively short DWCNTs. The DTB model can offer a much better prediction than the DEB model when the DWCNT is very short especially for high-order frequencies.

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Combined ReaxFF and Ab Initio MD Simulations of Brown Coal Oxidation and Coal–Water Interactions

Entropy ◽

10.3390/e24010071 ◽

2021 ◽

Vol 24 (1) ◽

pp. 71

Author(s):

Shi Yu ◽

Ruizhi Chu ◽

Xiao Li ◽

Guoguang Wu ◽

Xianliang Meng

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bonds ◽

Ab Initio ◽

Brown Coal ◽

Water Adsorption ◽

Md Simulations ◽

Dynamics Simulation ◽

Ab Initio Molecular Dynamics ◽

Coal Oxidation ◽

Simulation Results

In this manuscript, we use a combination of Car–Parrinello molecular dynamics (CPMD) and ReaxFF reactive molecular dynamics (ReaxFF-MD) simulations to study the brown coal–water interactions and coal oxidation. Our Car–Parrinello molecular dynamics simulation results reveal that hydrogen bonds dominate the water adsorption process, and oxygen-containing functional groups such as carboxyl play an important role in the interaction between brown coal and water. The discrepancy in hydrogen bonds formation between our simulation results by ab initio molecular dynamics (CPMD) and that by ReaxFF-MD indicates that the ReaxFF force field is not capable of accurately describing the diffusive behaviors of water on lignite at low temperatures. The oxidations of brown coal for both fuel rich and fuel lean conditions at various temperatures were investigated using ReaxFF-MD simulations through which the generation rates of major products were obtained. In addition, it was observed that the density decrease significantly enhances the generation of gaseous products due to the entropy gain by reducing system density. Although the ReaxFF-MD simulation of complete coal combustion process is limited to high temperatures, the combined CPMD and ReaxFF-MD simulations allow us to examine the correlation between water adsorption on brown coal and the initial stage of coal oxidation.

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Molecular Dynamic Simulations on the Compatibility of PP/PA12 Blends

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.633-634.270 ◽

2014 ◽

Vol 633-634 ◽

pp. 270-273 ◽

Cited By ~ 1

Author(s):

Min Zhang ◽

Guo Fang Zhang ◽

Yu Xi Jia

Keyword(s):

Molecular Dynamics ◽

Polymer Blends ◽

Md Simulation ◽

Md Simulations ◽

Solubility Parameters ◽

Molecular Dynamic Simulations ◽

Dynamic Simulations ◽

Cohesive Energy Density ◽

Pure Substances ◽

The Difference

The compatibilities of polymer blends, Polypropylene (PP) and Polyamide12(PA12), was simulated by molecular dynamics (MD) simulations. Density, cohesive energy density (CED) ,and solubility parameters (δ) of pure substances and PP/PA12 blends were calculated by MD simulations with the COMPASS force field for the prediction of polymer blends compatibility . Results showed that PP/PA12 is not miscrible by comparing the difference in the solubility parameter value ( Δδ), radial distribution function value. The predictions agreed well with the experimental results. So it can be showed that MD simulation is a valid method to provide information on miscibility of polymer blends.

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Wettability of organically coated tridymite surface – molecular dynamics study

Pure and Applied Chemistry ◽

10.1515/pac-2014-1103 ◽

2015 ◽

Vol 87 (4) ◽

pp. 405-413 ◽

Cited By ~ 2

Author(s):

Roland Šolc ◽

Daniel Tunega ◽

Martin H. Gerzabek ◽

Susanne K. Woche ◽

Jörg Bachmann

Keyword(s):

Molecular Dynamics ◽

Md Simulations ◽

Hydroxyl Groups ◽

Hydrophobic Contact ◽

Si Units ◽

Incomplete Coverage ◽

Modified Surface ◽

The Difference ◽

Silanized Silica ◽

Glass Surfaces

AbstractClassical molecular dynamics (MD) study was performed in order to explain a different wettability of silanized silica-glass surfaces prepared by using two different precursors – dichlorodimethylsilane (DCDMS) and dimethyldiethoxysilane (DMDES), respectively. Whereas the modified surface prepared by DCDMS becomes hydrophobic (contact angle (CA) of water >90°), DMDES-modified surface stays partially hydrophilic (CA ∼39°). In order to explain the observed discrepancy, several models of surfaces of trydimite with different coating by (CH3)2–Si= units were constructed and treated by water nanodroplets in the MD simulations. The models of surfaces differ by a different degree of surface coverage and/or oligomerized (CH3)2–Si= units in a lateral dimension. The simulations showed that incomplete coverage leads to a decrease of the computed CA, whereas upon lateral oligomerization the CA increases. This variation of the CA is directly related to the accessible amount of the hydroxyl groups on the surfaces and can be a possible explanation of the difference in wettability between DCDMS- and DMDES-treated glass surfaces.

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Molecular Dynamics Exploration of Selectivity of Dual Inhibitors 5M7, 65X, and 65Z toward Fatty Acid Binding Proteins 4 and 5

International Journal of Molecular Sciences ◽

10.3390/ijms19092496 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2496 ◽

Cited By ~ 18

Author(s):

Fangfang Yan ◽

Xinguo Liu ◽

Shaolong Zhang ◽

Jing Su ◽

Qinggang Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Fatty Acid ◽

Binding Proteins ◽

Metabolic Diseases ◽

Md Simulations ◽

Van Der Waals Interactions ◽

Fatty Acid Binding Proteins ◽

Fatty Acid Binding ◽

Free Energy Decomposition ◽

The Difference

Designing highly selective inhibitors of fatty acid binding proteins 4 and 5 (FABP4 and FABP5) is of importance for treatment of some diseases related with inflammation, metabolism, and tumor growth. In this study, molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were performed to probe binding selectivity of three inhibitors (5M7, 65X, and 65Z) to FABP4/FABP5 with Ki values of 0.022/0.50 μM, 0.011/0.086 μM, and 0.016/0.12 μM, respectively. The results not only suggest that all inhibitors associate more tightly with FABP4 than FABP5, but also prove that the main forces driving the selective bindings of inhibitors to FABP4 and FABP5 stem from the difference in the van der Waals interactions and polar interactions of inhibitors with two proteins. Meanwhile, a residue-based free energy decomposition method was applied to reveal molecular basis that inhibitors selectively interact with individual residues of two different proteins. The calculated results show that the binding difference of inhibitors to the residues (Phe16, Phe19), (Ala33, Gly36), (Phe57, Leu60), (Ala75, Ala78), (Arg126, Arg129), and (Tyr128, Tyr131) in (FABP4, FABP5) drive the selectivity of inhibitors toward FABP4 and FABP5. This study will provide great help for further design of effective drugs to protect against a series of metabolic diseases, arteriosclerosis, and inflammation.

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Efficient Treatment of Fixed and Induced Dipolar Interactions

MRS Proceedings ◽

10.1557/proc-653-z7.22 ◽

2000 ◽

Vol 653 ◽

Author(s):

Celeste Sagui ◽

Thoma Darden

Keyword(s):

Molecular Dynamics ◽

Md Simulations ◽

Lagrangian Formalism ◽

Dipolar Interactions ◽

Time Step ◽

Efficient Treatment ◽

Particle Mesh Ewald ◽

Fixed Charges ◽

Self Consistency ◽

Induced Dipoles

AbstractFixed and induced point dipoles have been implemented in the Ewald and Particle-Mesh Ewald (PME) formalisms. During molecular dynamics (MD) the induced dipoles can be propagated along with the atomic positions either by interation to self-consistency at each time step, or by a Car-Parrinello (CP) technique using an extended Lagrangian formalism. The use of PME for electrostatics of fixed charges and induced dipoles together with a CP treatment of dipole propagation in MD simulations leads to a cost overhead of only 33% above that of MD simulations using standard PME with fixed charges, allowing the study of polarizability in largemacromolecular systems.

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Structure, Stability and Water Adsorption on Ultra-Thin TiO2 Supported on TiN

10.26434/chemrxiv.8425367.v1 ◽

2019 ◽

Author(s):

Jose Julio Gutierrez Moreno ◽

Marco Fronzi ◽

Pierre Lovera ◽

alan O'Riordan ◽

Mike J Ford ◽

...

Keyword(s):

Density Functional ◽

Water Adsorption ◽

Chemical Potential ◽

Energy Gap ◽

Molecular Water ◽

Structure Stability ◽

Ambient Conditions ◽

Rutile Structure ◽

The Stability ◽

The One

Interfacial metal-oxide systems with ultrathin oxide layers are of high interest for their use in catalysis. In this study, we present a density functional theory (DFT) investigation of the structure of ultrathin rutile layers (one and two TiO2 layers) supported on TiN and the stability of water on these interfacial structures. The rutile layers are stabilized on the TiN surface through the formation of interfacial Ti–O bonds. Charge transfer from the TiN substrate leads to the formation of reduced Ti3+ cations in TiO2. The structure of the one-layer oxide slab is strongly distorted at the interface, while the thicker TiO2 layer preserves the rutile structure. The energy cost for the formation of a single O vacancy in the one-layer oxide slab is only 0.5 eV with respect to the ideal interface. For the two-layer oxide slab, the introduction of several vacancies in an already non-stoichiometric system becomes progressively more favourable, which indicates the stability of the highly non-stoichiometric interfaces. Isolated water molecules dissociate when adsorbed at the TiO2 layers. At higher coverages the preference is for molecular water adsorption. Our ab initio thermodynamics calculations show the fully water covered stoichiometric models as the most stable structure at typical ambient conditions. Interfacial models with multiple vacancies are most stable at low (reducing) oxygen chemical potential values. A water monolayer adsorbs dissociatively on the highly distorted 2-layer TiO1.75-TiN interface, where the Ti3+ states lying above the top of the valence band contribute to a significant reduction of the energy gap compared to the stoichiometric TiO2-TiN model. Our results provide a guide for the design of novel interfacial systems containing ultrathin TiO2 with potential application as photocatalytic water splitting devices.

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Split the Charge Difference in Two! a Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations

10.26434/chemrxiv.9783155.v2 ◽

2020 ◽

Author(s):

Matías R. Machado ◽

Sergio Pantano

Keyword(s):

Molecular Dynamics ◽

Ionic Strength ◽

Molecular Simulations ◽

Md Simulations ◽

Good Practices ◽

Rule Of Thumb ◽

Ionic Concentrations

Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD) simulations, methods or practical rules to set ionic strength are scarce and rarely documented. Based on a recently proposed thermodynamics method we provide an accurate rule of thumb to define the electrolytic content in simulation boxes. Extending the use of good practices in setting up MD systems is promptly needed to ensure reproducibility and consistency in molecular simulations.

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