scholarly journals Structural and Dynamic Properties of Hydrophobic Eutectic Solvents Based on Menthol and Fatty Acids: a Molecular Dynamics Simulation Study

2021 ◽  
Author(s):  
Samaneh Barani Pour ◽  
Jaber Jahanbin Sardroodi ◽  
Alireza Rastkar Ebrahimzadeh
Keyword(s):  
Molecular Dynamics ◽  
Fatty Acids ◽  
Dynamic Properties ◽  
Mean Square Displacement ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Eutectic Mixtures ◽  
Dynamical Properties ◽  
Reorientation Dynamics ◽  
Dynamics Simulations

Abstract The structural and dynamical properties of the binary mixture of Menthol (MEN) and Fatty acids (FAs) were investigated using molecular dynamics simulations. We focused on the relationship between the structural and dynamical properties of the eutectic mixtures of MEN and FAs with different molar percentages of FAs. Structural properties of the eutectic mixtures were characterized by calculating the combined distribution functions(CDFs), the radial distribution functions (RDFs), and the angular distribution functions (ADFs), and the Hydrogen bonding network between species and Spatial distribution functions (SDF). Further interaction between menthol and Caprylic acid molecules was confirmed by the results of these analyzes. Also, the transport properties of the mixtures were investigated by using the mean square displacement (MSD) of the centers of mass of the species, self-diffusion coefficients and vector reorientation dynamics (VRD) of bonds. The simulation results indicated that intermolecular interactions have a significant effect on the dynamic properties of species.

scholarly journals The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5403
Author(s):  
Hangxin Liu ◽  
Shuqing Xiang ◽  
Haomiao Zhu ◽  
Li Li
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Biological Significance ◽  
Mean Square Displacement ◽  
Chemical Properties ◽  
Dynamics Simulation ◽  
Hydration Water ◽  
Total Change ◽  
Dynamical Properties ◽  
Dynamics Simulations

The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.

Solvation of cholesterol in different solvents: a molecular dynamics simulation study

2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dimethyl Sulfoxide ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Dynamical Properties ◽  
Dynamics Simulations

Molecular dynamics simulations were applied to an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, to gain insights into the structural and dynamical properties.

Molecular Dynamics Study of the Structural and Dynamical Properties of Liquid Tetrahydrofuran

1990 ◽  
Vol 45 (11-12) ◽  
pp. 1342-1344 ◽  
Author(s):  
W. Drabowicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Radial Distribution ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Radial Distribution Functions ◽  
Frequency Spectra ◽  
Autocorrelation Functions ◽  
Dynamical Properties

AbstractA molecular dynamics simulation has been performed to investigate the structural and dynamical properties of liquid tetrahydrofuran. In particular, we have calculated six radial distribution functions, translational and rotational autocorrelation functions and their associated frequency spectra.

Molecular dynamics simulation of aggregation of monocrystal and polycrystal copper nanoparticles

2019 ◽  
Vol 33 (16) ◽  
pp. 1950168
Author(s):  
Linxing Zhang ◽  
Guang Hong ◽  
Shouyin Cai
Keyword(s):  
Molecular Dynamics ◽  
Lattice Structure ◽  
Displacement Vector ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Gyration Radius ◽  
Mean Square ◽  
Shrinkage Ratio ◽  
Lower Temperature ◽  
Dynamics Simulations

Molecular dynamics simulations were employed to investigate the aggregation of monocrystal and polycrystal nanoparticles. The lattice structure, displacement vector, potential energy, shrinkage ratio, relative gyration radius and mean square displacement of the two systems are compared. The results indicate that the aggregation of polycrystal nanoparticles is more drastic than that of monocrystal nanoparticles. Besides, the polycrystal nanoparticles are found contacted and melted at lower-temperature than that of monocrystal nanoparticles. The reason for all these phenomena is that there is additional surface energy in the grain boundary of polycrystal nanoparticles.

Structure and Dynamics of NaCl in Methanol. A Molecular Dynamics Study

1991 ◽  
Vol 46 (10) ◽  
pp. 887-897 ◽  
Author(s):  
D. Marx ◽  
K. Heinzinger ◽  
G. Pálinkás ◽  
I. Bakó
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Nacl Solution ◽  
Geometrical Arrangement ◽  
Self Diffusion ◽  
Site Model ◽  
Structure And Dynamics ◽  
Dynamical Properties

AbstractA recently developed flexible three-site model for methanol was employed to perform a Molecular Dynamics simulation of a 0.6 molal NaCl solution. The ion-methanol and ion-ion potential functions were derived from ab initio calculations. The structural properties of the solution are discussed on the basis of radial and angular distribution functions, the orientation of the methanol molecules, and their geometrical arrangement in the solvation shells of the ions. The dynamical properties of the solution - like self-diffusion coefficients, hindered translations, librations, and internal vibrations of the methanol molecules - are calculated from various autocorrelation functions.

A Molecular Dynamics Simulation of the Transport Properties of Molten (La1/3, K)Cl

2005 ◽  
Vol 60 (3) ◽  
pp. 187-192 ◽  
Author(s):  
Masahiko Matsumiya ◽  
Koichi Seo
Keyword(s):  
Molecular Dynamics ◽  
Charge Asymmetry ◽  
The Self ◽  
Dynamics Simulation ◽  
Alkali Chloride ◽  
Self Diffusion ◽  
Dynamical Properties ◽  
Experimental Values ◽  
Dynamics Simulations ◽  
Self Diffusion Coefficient

Molecular dynamics simulations of molten (La1/3, K)Cl at 1123 K have been performed in order to investigate the correlation between simulated dynamical properties such as the self-exchange velocity (ν), the self-diffusion coefficient (D) and the electrical conductivity (κ) and the corresponding experimental values. The simulated results revealed that v and D of potassium decrease with increasing mole fraction of lanthanum, as expected from the experimental internal cation mobilities, b. The decrease of bK, νK and DK is ascribed to the tranquilization effect by La3+, which strongly interacts with Cl−. In contrast, bLa, νLa, and DLa increase with increasing concentration of La3+. The distorted linkage of the network structure of [LaCl6]3− units was disconnected with increasing the concentration of the alkali chloride. This might be attributed to the stronger association of La3+ with Cl− due to the enhanced charge asymmetry of the two cations neighboring Cl−. The sequence of the calculated v’s, D’s, and κ’s is consistent with those of the referred experimental results.

Molecular Dynamics Simulation of the Glass Transition of Ortho-Terphenyl in Bulk and Thin Films

2006 ◽  
Vol 924 ◽  
Author(s):  
Jayeeta Ghosh ◽  
Roland Faller
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
A Priori ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Technological Advancement ◽  
Atomistic Model ◽  
Reorientation Dynamics ◽  
Bulk Model ◽  
Dynamics Simulations

ABSTRACTThe glass transition temperature in thin film depends strongly on film thickness and interaction with the substrate and it is normally a priori not clear which way it deviates from the bulk value. This causes new challenge in the technological advancement of smaller and smaller electronic devices. In this study molecular dynamics simulations of a low-molecular weight organic glass former, ortho-terphenyl, are carried out in bulk and freestanding films. The main motivation is to provide insight into the confinement effect without interface interactions. Based on earlier models of ortho-terphenyl we developed an atomistic model for bulk simulations. The model reproduces the literature data from simulations as well as experiments. After characterizing the bulk model we form a freestanding film. This film gives us the opportunity to study the dynamical heterogeneity near the glass transition by in-plane mobility and reorientation dynamics. We also develop a structurally coarse-grained model for this glass former based on our atomistic model to study bigger system for a longer period of time.

scholarly journals A Study of the Adsorption and Diffusion Behavior of a Single Polydimethylsiloxane Chain on a Silicon Surface by Molecular Dynamics Simulation

2011 ◽  
Vol 391-392 ◽  
pp. 998-1002
Author(s):  
Jian Quan Li ◽  
Dan Mu
Keyword(s):  
Molecular Dynamics ◽  
Adsorption Energy ◽  
Dynamic Properties ◽  
Relative Dielectric Constant ◽  
Degree Of Polymerization ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Chain Lengths ◽  
The Relationship ◽  
And Diffusion

The adsorption and diffusion of polydimethylsiloxane (PDMS) with different chain lengths on a silicon (111) surface were studied by molecular dynamics simulations. The relative dielectric constant was selected to be 1 to mimic a vacuum. The chains were all present as two dimensional (2D) adsorption conformation on the surface but different conformations and dynamic properties were found in the two absolutely different environments. The relationship between the adsorption energy of the different chain lengths and the degree of polymerization follows a linear function and the average adsorption energy per segment is -0.42 kcal/mol. In addition, the diffusion coefficient (D) of these chains scales with the degree of polymerization (N) as N-3/2.

scholarly journals Molecular Dynamics Simulation of Polyacrylamide Adsorption on Cellulose Nanocrystals

Nanomaterials ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1256 ◽  
Author(s):  
Darya Gurina ◽  
Oleg Surov ◽  
Marina Voronova ◽  
Anatoly Zakharov
Keyword(s):  
Molecular Dynamics ◽  
Cellulose Nanocrystals ◽  
Water Environment ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Radial Distribution Functions ◽  
Dynamical Characteristics ◽  
Polymer Interactions ◽  
Dynamics Simulations

Classical molecular dynamics simulations of polyacrylamide (PAM) adsorption on cellulose nanocrystals (CNC) in a vacuum and a water environment are carried out to interpret the mechanism of the polymer interactions with CNC. The structural behavior of PAM is studied in terms of the radius of gyration, atom–atom radial distribution functions, and number of hydrogen bonds. The structural and dynamical characteristics of the polymer adsorption are investigated. It is established that in water the polymer macromolecules are mainly adsorbed in the form of a coil onto the CNC facets. It is found out that water and PAM sorption on CNC is a competitive process, and water weakens the interaction between the polymer and CNC.

scholarly journals Dynamic and Static Properties of Aqueous NaCl Solutions at 25°C as a Function of NaCl Concentration: A Molecular Dynamics Simulation Study

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Song Hi Lee
Keyword(s):  
Molecular Dynamics ◽  
Radial Distribution ◽  
Dynamic Properties ◽  
Md Simulations ◽  
Distribution Functions ◽  
Molar Conductivity ◽  
Dynamics Simulation ◽  
Radial Distribution Functions ◽  
Deep Minimum ◽  
Nacl Concentration

We present the result of molecular dynamics (MD) simulations to calculate the molar conductivity Λ m =   λ N a + +   λ C l − of NaCl in SPC/E water at 25°C as a function of NaCl concentration (c) using Ewald sums employing a velocity Verlet algorithm. It is found that the MD result for Λm with Ewald sum parameter κ = 0.10 Å−1 gives the closest one to the experimental data and that the obtained radial distribution functions g i i (r) with κ = 0.10 Å−1 show a dramatic change with a very deep minimum of g NaCl (r) and, as a result, sharp maxima of g NaNa (r) and g ClCl (r) at the distance 9.95 Å, which indicates a characteristic of ionic atmosphere, the basis of the Debye–Hückel theory of ionic solutions. The static and dynamic properties of NaCl (aq) solutions are analyzed in terms of radial distribution functions, hydration numbers, coordination numbers around Na+ and Cl−, residence times of water around Na+ and Cl−, water diffusion, and ion-ion electrostatic energies to explain the behavior of the molar conductivity Λm of NaCl obtained from our MD simulations.

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