scholarly journals A Molecular Dynamics Study on the Mechanism of Adsorption of Phenol and P-Nitrophenol on Kaolinite Surface

2020 ◽  
Author(s):  
Danish Khan ◽  
Jyoti Kuntail ◽  
Indrajit Sinha
Keyword(s):  
Molecular Dynamics ◽  
Organic Pollutants ◽  
Adsorption Isotherms ◽  
Freundlich Isotherm ◽  
Md Simulations ◽  
Distribution Functions ◽  
Isotherm Models ◽  
Phase Point ◽  
Dilute Aqueous Solution ◽  
Kaolinite Surface

Herein, we investigate the adsorption of two organic pollutants, phenol and p-nitrophenol (PNP) in dilute aqueous solution conditions on kaolinite (001) surface through classical molecular dynamics (MD) simulations. The present investigation addresses both adsorption isotherms and mechanistic issues. MD simulations at different solute concentrations generated density profiles and, thereby, adsorption isotherms. The data generated for phenol adsorption fitted both Langmuir and Freundlich isotherm models equally well. Alternatively, PNP adsorption data on the kaolinite surface followed the Langmuir model better. Overall, phenol exhibits higher adsorption capacity on kaolinite than PNP. These results confirm to the experimental observations made by earlier publications in the literature. Radial distribution functions (RDF) between various atom types on the adsorbent and molecules in the solution phase point towards a hydrogen bond dominated interaction mechanisms for organic pollutants.

scholarly journals A Molecular Dynamics Study on the Mechanism of Adsorption of Phenol and P-Nitrophenol on Kaolinite Surface

2020 ◽  
Author(s):  
Danish Khan ◽  
Jyoti Kuntail ◽  
Indrajit Sinha
Keyword(s):  
Molecular Dynamics ◽  
Organic Pollutants ◽  
Adsorption Isotherms ◽  
Freundlich Isotherm ◽  
Md Simulations ◽  
Distribution Functions ◽  
Isotherm Models ◽  
Phase Point ◽  
Dilute Aqueous Solution ◽  
Kaolinite Surface

Herein, we investigate the adsorption of two organic pollutants, phenol and p-nitrophenol (PNP) in dilute aqueous solution conditions on kaolinite (001) surface through classical molecular dynamics (MD) simulations. The present investigation addresses both adsorption isotherms and mechanistic issues. MD simulations at different solute concentrations generated density profiles and, thereby, adsorption isotherms. The data generated for phenol adsorption fitted both Langmuir and Freundlich isotherm models equally well. Alternatively, PNP adsorption data on the kaolinite surface followed the Langmuir model better. Overall, phenol exhibits higher adsorption capacity on kaolinite than PNP. These results confirm to the experimental observations made by earlier publications in the literature. Radial distribution functions (RDF) between various atom types on the adsorbent and molecules in the solution phase point towards a hydrogen bond dominated interaction mechanisms for organic pollutants.

scholarly journals Adsorption-Kinetic Studies of Mordant Exhaust Dyeing of Cotton and Silk Fabrics with Dye Extract of M. lucida Plant Species

2021 ◽  
Vol 75 ◽  
Author(s):  
Janani Loum ◽  
Robert Byamukama ◽  
P.A.G. Wanyama
Keyword(s):  
Adsorption Isotherms ◽  
Freundlich Isotherm ◽  
Kinetic Studies ◽  
Isotherm Models ◽  
Freundlich Model ◽  
Reaction Orders ◽  
Dyed Fabrics ◽  
Silk Fabrics ◽  
Exhaust Dyeing ◽  
Traditional Natural

ABSTRACT The kinetics and adsorption isotherms of the extremely slow traditional natural exhaust dyeing that takes many hours or days have been studied purposely to find means of improving the process. The dyeing of cotton and silk fabrics using dye extract of M. lucida at 50 °C were elucidated with graphs to predict the reaction orders and identify the appropriate adsorption isotherm model(s). Since the dye is UV active, changes in UV absorbance were used in place of changes in concentrations. The simultaneous and post mordanting methods followed pseudo-second-order reactions, hence chemisorption. However, mordant application to the dyed fabrics during post mordant followed a pseudo-first-order model, largely physisorption. Dyeing has followed Langmuir and Freundlich isotherm models with linear correlation r2 ranging between 1 and 0.998. From the Freundlich model and values of Langmuir constant RL (0.9307 to 1.0), the process is homogeneous, forming a favourable and linear monolayer. Accordingly, the dyeing speed can be improved by increasing the concentration of dye liquor. Additionally, according to the Freundlich model, higher dye intensity on fabrics is recorded in post mordanting. Keywords: adsorption isotherms, equilibrium, exhaust dyeing, mordant, rate law

Molecular Dynamics Simulation to Study the Effect of Empirical Potential Functions on Modeling of Diamond-Like Carbon

2013 ◽  
Author(s):  
Longqiu Li ◽  
Ming Xu ◽  
Wenping Song ◽  
Guangyu Zhang ◽  
Andrey Ovcharenko
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Carbon ◽  
Md Simulations ◽  
Distribution Functions ◽  
Dynamics Simulation ◽  
Empirical Potential ◽  
Mechanical And Tribological Properties ◽  
Empirical Potentials ◽  
Rebo Potential ◽  
Quenching Method

Molecular dynamics (MD) simulations is an effective method to investigate the mechanical and tribological properties of amorphous carbon since the coordinates of all atoms can be calculated as a function of time. Several empirical potentials can be used to model the interatomic interactions of carbon atoms, including the Tersoff potential, the Reactive Bond Order (REBO) potential and its revised versions, and the Reactive Force Field (ReaxFF) potential. The choice of empirical potential is one of the fundamental and important assumptions in the MD approach since it can affect the properties of amorphous carbon during the MD simulations. In this study, liquid quenching method is used to model amorphous carbon for computational efficiency. We will study the influence of the three types of potentials, specifically the Tersoff potential, the 2nd REBO potential and the ReaxFF potential on DLC parameters. These parameters include the sp3 content as a function of density, the arrangement of the amorphous carbon atoms, hybridization and the radial distribution functions G(r).

Structural properties of liquid aluminosilicate with varying Al2O3/SiO2 ratios: Insight from analysis and visualization of molecular dynamics data

2017 ◽  
Vol 31 (05) ◽  
pp. 1750036 ◽  
Author(s):  
N. V. Yen ◽  
M. T. Lan ◽  
L. T. Vinh ◽  
N. V. Hong
Keyword(s):  
Molecular Dynamics ◽  
Random Network ◽  
Md Simulations ◽  
Degree Of Polymerization ◽  
Distribution Functions ◽  
Molar Ratio ◽  
Nonbridging Oxygen ◽  
Structural Units ◽  
Self Diffusion ◽  
Continuous Random Network

Molecular dynamics (MD) simulations and visualizations were explored to investigate the changes in structure of liquid aluminosilicates. The models were constructed for four compositions with varying Al2O3/SiO2 ratio. The local structure and network topology was analyzed through the pair of radial distribution functions, bond angle, bond length and coordination number distributions. The results showed that the structure of aluminosilicates mainly consists of the basic structural units TO[Formula: see text] (T is Al or Si; y = 3, 4, 5). Two adjacent units TO[Formula: see text] are linked to each other through common oxygen atoms and form continuous random network of basic structural units TO[Formula: see text]. The bond statistics (corner-, edge- and face- sharing) between two adjacent TO[Formula: see text] units are investigated in detail. The self-diffusion coefficients for three atomic types are affected by the degree of polymerization (DOP) of network characterized by the proportions of nonbridging oxygen (NBO) and Q[Formula: see text] species in the system. It was found that Q4 and Q3 tetrahedral species (tetrahedron with four and three bridging oxygens, respectively) decreases, while Q0 (with four nonbridging oxygen) increase with increasing Al2O3/SiO2 molar ratio, suggesting that a less polymerized network was formed. The structural and dynamical heterogeneities, micro-phase separation and liquid–liquid phase transition are also discussed in this work.

scholarly journals Investigation of the reactivity properties of a thiourea derivative with anticancer activity by DFT, MD simulations

2021 ◽  
Author(s):  
Sheena Mary ◽  
Y. Shyma Mary ◽  
Anna Bielenica ◽  
Stevan Armaković ◽  
Sanja J. Armaković ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Density Functional ◽  
Spectroscopic Analysis ◽  
Md Simulations ◽  
Distribution Functions ◽  
Solubility Parameters ◽  
Functional Theory ◽  
Quantum Molecular Descriptors ◽  
Combined Application ◽  
Local Reactivity

Abstract Spectroscopic analysis of 1-(2-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (FPTT) is reported. Experimental and theoretical analysis of FPTT, with Molecular Dynamics (MD) simulations, are reported for finding different parameters like: identification of suitable excipients, interactions with water, and sensitivity towards autoxidation. Molecular dynamics and docking show that FPTT can act as a potential inhibitor for new drug. Additionally, local reactivity, interactivity with water, and compatibility of FPTT molecule with frequently used excipients have been studied by combined application of density functional theory (DFT) and MD simulations. Analysis of local reactivity has been performed based on selected fundamental quantum-molecular descriptors, while interactivity with water was studied by calculations of radial distribution functions (RDFs). Compatibility with excipients has been assessed through calculations of solubility parameters, applying MD simulations.

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.

scholarly journals Removal of Cd(II) and Cu(II) from Aqueous Solution by Na+-Modified Pisha Sandstone

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Xia Wang ◽  
Yongxing Cui ◽  
Qi Peng ◽  
Chenbin Fan ◽  
Zhiqin Zhang ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Adsorption Isotherms ◽  
Freundlich Isotherm ◽  
Environmental Issues ◽  
Isotherm Models ◽  
Mining Areas ◽  
Endothermic Reactions ◽  
Pseudo Second Order ◽  
Ph Range ◽  
Open Cast

Heavy metals have caused serious environmental issues, which are enriched during open-cast coal mining. It is urgent to develop sustainable remediation materials to protect and restore the contaminated soil and aquifers in mining areas. The feasibility of applying Pisha sandstone (PS) and Na+-modified Pisha sandstone (Na-PS) for adsorption of heavy metals was evaluated. Na-PS exhibited maximum Cd(II) and Cu(II) removal rates of 65.9% and 99.8%, respectively, exceeding the corresponding values for PS (8.2% and 1.3%, respectively) in 1 × 10−3 M solution. Efficient heavy metals adsorption occurred in the pH range 5.0–6.0. The adsorption of Cu(II) and Cd(II) on PS and Na-PS was characterized by kinetic models and adsorption isotherms and was well represented by pseudo-second-order kinetics (R2 > 0.99) and the Langmuir and Freundlich isotherm models. The values of the thermodynamic parameters indicated that the interactions were spontaneous endothermic reactions. Binary solutions adsorption isotherms indicated that the linearity of the adsorption amount and initial concentration of Cu(II) and Cd(II) was better in certain ranges and the adsorbents were selective towards Cu(II) rather than Cd(II). Therefore, PSs can be used as excellent adsorbents for Cu(II) and Cd(II) remediation from contaminated surface water.

Efficient Treatment of Fixed and Induced Dipolar Interactions

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.

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

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

<p> 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.</p>

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