scholarly journals Dynamic Properties of Water Confined in Graphene-Based Membrane: A Classical Molecular Dynamics Simulation Study

Membranes ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 165 ◽  
Author(s):  
One-Sun Lee
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Free Energy ◽  
Graphene Sheets ◽  
Water Molecules ◽  
Energy Profile ◽  
Confined Water ◽  
Graphene Surface ◽  
Dynamics Simulations ◽  
Density Of Water

We performed molecular dynamics simulations of water molecules inside a hydrophobic membrane composed of stacked graphene sheets. By decreasing the density of water molecules inside the membrane, we observed that water molecules form a droplet through a hydrogen bond with each other in the hydrophobic environment that stacked graphene sheets create. We found that the water droplet translates as a whole body rather than a dissipate. The translational diffusion coefficient along the graphene surface increases as the number of water molecules in the droplet decreases, because the bigger water droplet has a stronger van der Waals interaction with the graphene surface that hampers the translational motion. We also observed a longer hydrogen bond lifetime as the density of water decreased, because the hydrophobic environment limits the libration motion of the water molecules. We also calculated the reorientational correlation time of the water molecules, and we found that the rotational motion of confined water inside the membrane is anisotropic and the reorientational correlation time of confined water is slower than that of bulk water. In addition, we employed steered molecular dynamics simulations for guiding the target molecule, and measured the free energy profile of water and ion penetration through the interstice between graphene sheets. The free energy profile of penetration revealed that the optimum interlayer distance for desalination is ~10 Å, where the minimum distance for water penetration is 7 Å. With a 7 Å interlayer distance between the graphene sheets, water molecules are stabilized inside the interlayer space because of the van der Waals interaction with the graphene sheets where sodium and chloride ions suffer from a 3–8 kcal/mol energy barrier for penetration. We believe that our simulation results would be a significant contribution for designing a new graphene-based membrane for desalination.

Molecular Dynamics Study of Interfacial Thermal Resistance of Mercapto-Alkanol Self-Assembled Monolayer and Water

2009 ◽  
Author(s):  
Touru Kawaguchi ◽  
Gota Kikugawa ◽  
Ikuya Kinefuchi ◽  
Taku Ohara ◽  
Shinichi Yatuzuka ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Thermal Resistance ◽  
Chem Phys ◽  
Nonequilibrium Molecular Dynamics ◽  
Interfacial Thermal Resistance ◽  
Water Molecules ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
Dynamics Simulations

The interfacial thermal resistance of 11-mercaptoundecanol (-S(CH2)11OH) self-assembled monolayer (SAM) adsorbed on Au(111) substrate and water was investigated using nonequilibrium molecular dynamics simulations. The interfacial thermal resistance was found to be a half of that in the system which consists of 1-dodecanthiol (-S(CH2)11CH3) SAM adsorbed on Au(111) and toluene [Kikugawa G. et al., J. Chem. Phys. (2009)]. The effective thermal energy transfer originates from hydrogen-bond structure between the SAM and water molecules in spite of weak structurization of water molecules near the SAM surface.

scholarly journals Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers

2014 ◽  
Vol 126 (3) ◽  
pp. 637-647 ◽  
Author(s):  
YOUSEF NADEMI ◽  
SEPIDEH AMJAD IRANAGH ◽  
ABBAS YOUSEFPOUR ◽  
SEYEDEH ZAHRA MOUSAVI ◽  
HAMID MODARRESS
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Energy Profile ◽  
Free Energy Profile ◽  
Dynamics Simulations

Thermodynamic, structural, and dynamical properties of nano-confined water using SPC/E and TIP4P models by molecular dynamics simulations

2018 ◽  
Vol 42 (19) ◽  
pp. 16258-16272 ◽  
Author(s):  
Elham Jalalitalab ◽  
Mohsen Abbaspour ◽  
Hamed Akbarzadeh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Molecules ◽  
Confined Water ◽  
Dynamical Properties ◽  
Dynamics Simulations

Different morphologies of water molecules are confined between two parallel graphene surfaces.

scholarly journals Tumbling with a limp: local asymmetry in water's hydrogen bond network and its consequences

2020 ◽  
Vol 22 (19) ◽  
pp. 10397-10411 ◽  
Author(s):  
Hossam Elgabarty ◽  
Thomas D. Kühne
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Liquid Water ◽  
Decomposition Analysis ◽  
Energy Decomposition Analysis ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Energy Decomposition ◽  
Bond Network ◽  
Dynamics Simulations

Ab initio molecular dynamics simulations of ambient liquid water and energy decomposition analysis have recently shown that water molecules exhibit significant asymmetry between the strengths of the two donor and/or the two acceptor interactions.

scholarly journals Atomistic molecular dynamics insights on water local structure and dynamics on different surfaces of zeolitic-imidazolate frameworks

2021 ◽  
Author(s):  
Mohammad R. Momeni ◽  
Dil K. Limbu ◽  
Sara Abdelhamid ◽  
Shaina Pearson ◽  
Farnaz A. Shakib
Keyword(s):  
Molecular Dynamics ◽  
Outer Surface ◽  
Defect Formation ◽  
Intermolecular Hydrogen Bond ◽  
Water Molecules ◽  
Confined Water ◽  
Zeolitic Imidazolate Frameworks ◽  
Small Pore ◽  
Bulk Model ◽  
Dynamics Simulations

Most of chemistry in nanoporous materials with small pore sizes and windows is known to occur on the surface which is in immediate contact with substrate/solvent, rather than inside pores and channels. Here, we report the results of our comprehensive atomistic molecular dynamics simulations on deciphering the intermolecular hydrogen bond network of water on outer surface of a nanoparticle model of ZIF-8 vs. inner surfaces of its pristine crystalline bulk model. Using a finite ~5.1 nm nanoparticle model with edges containing under--coordinated Zn2+ metal sites we show that water exposed to the surface of the nanoparticle exhibits both interfacial and bulk-like characters. Furthermore, we illustrate that as water content increases larger droplets are formed with water molecules starting to diffuse into the nanopores. While the confined water in the crystalline bulk simulations is pushed to the vacant pores due to hydrophobic inner surfaces, the outer surface water molecules form chemical bonds with under--coordinated Zn2+ metal sites which act as nucleation sites for the water droplets to form and hence making the surface hydrophilic. By adapting a similar mechanism to the dangling linker defect formation mechanism, we probe the tendency of the outer surface of ZIF-8 nanoparticles to water attack and hydrolysis. Results presented in this work are useful in designing more robust materials for applications in humid environments.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

Sign in / Sign up

Export Citation Format

Share Document