scholarly journals Adsorption of metallic ions from aqueous solution on surfactant aggregates: a molecular dynamics study

2021 ◽  
Vol 24 (2) ◽  
pp. 23601
Author(s):  
E. H. Chavez-Martinez ◽  
E. Cedillo-Cruz ◽  
H. Dominguez
Keyword(s):  
Molecular Dynamics ◽  
Electrostatic Interactions ◽  
Sodium Dodecyl ◽  
Lead Sulfate ◽  
Distribution Functions ◽  
Metallic Ions ◽  
Positive Ions ◽  
Surfactant Aggregates ◽  
Aluminum Ions ◽  
Dynamics Simulations

Metallic ion adsorption on surfactant aggregates were studied with Molecular dynamics simulations. Using ionic salts, such as lead sulfate (PbSO4) and aluminum sulfate [Al2(SO4)3], adsorption of lead and aluminum were investigated at different salt concentrations and different surfactant aggregates (micelles) sizes. The micelles were constructed with spherical shapes composed of sodium dodecyl sulfate (SDS) anionic surfactants. The electrostatic interactions between the positive ions and the negative SDS headgroups promote capture of the metal particles on the aggregate surface. Metal adsorption was analyzed in terms of radial density profiles, partial pair distribution functions and adsorption isotherms. It is showed that SDS micelles adsorb better lead than aluminum ions regardless of the size of the aggregates and salt concentrations.

scholarly journals CO2 adsorption on a modified graphite surface with sodium dodecyl sulfate surfactants: A molecular dynamics study

2018 ◽  
Vol 65 (1) ◽  
pp. 20
Author(s):  
Héctor Domínguez Castro ◽  
Hugo Espinosa-Jiménez
Keyword(s):  
Molecular Dynamics ◽  
Sodium Dodecyl Sulfate ◽  
Gas Adsorption ◽  
Sodium Dodecyl ◽  
Co2 Concentration ◽  
Distribution Functions ◽  
Graphite Surface ◽  
Graphite Plate ◽  
Dodecyl Sulfate ◽  
Dynamics Simulations

Molecular dynamics simulations were carried out to study adsorption of CO2 on agraphite surface at different gas concentrations. It was observed a decrement in the adsorption on the graphite surface as the CO2 concentration increased. When the graphite surface was modified by the presence of surfactant molecules, sodium dodecyl sulfate (SDS), the results indicated that gas adsorption increased with respect to the system without SDS. Analysis of density profiles were used to characterise adsorption and langmuir isotherms constructed for the systems with and without SDS-modified surfaces. Interactions between the graphite plate and CO2 were investigated in terms of pair distribution functions.

scholarly journals Origin and control of ionic hydration patterns in nanopores

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Miraslau L. Barabash ◽  
William A. T. Gibby ◽  
Carlo Guardiani ◽  
Alex Smolyanitsky ◽  
Dmitry G. Luchinsky ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Water Molecules ◽  
Surrounding Water ◽  
Ionic Hydration ◽  
Hydration Shells ◽  
Water Layers ◽  
Dynamics Simulations ◽  
And Control

AbstractIn order to permeate a nanopore, an ion must overcome a dehydration energy barrier caused by the redistribution of surrounding water molecules. The redistribution is inhomogeneous, anisotropic and strongly position-dependent, resulting in complex patterns that are routinely observed in molecular dynamics simulations. Here, we study the physical origin of these patterns and of how they can be predicted and controlled. We introduce an analytic model able to predict the patterns in a graphene nanopore in terms of experimentally accessible radial distribution functions, giving results that agree well with molecular dynamics simulations. The patterns are attributable to a complex interplay of ionic hydration shells with water layers adjacent to the graphene membrane and with the hydration cloud of the nanopore rim atoms, and we discuss ways of controlling them. Our findings pave the way to designing required transport properties into nanoionic devices by optimising the structure of the hydration patterns.

scholarly journals Effects of temperatures on pressure-induced structural changes in amorphous Si: A molecular-dynamics study

10.29007/6kp3 ◽  
2020 ◽  
Author(s):  
Renji Mukuno ◽  
Manabu Ishimaru
Keyword(s):  
Molecular Dynamics ◽  
Phase Transformation ◽  
Amorphous Phase ◽  
Structural Changes ◽  
Interatomic Potential ◽  
Activation Barrier ◽  
Distribution Functions ◽  
High Density ◽  
Angle Distribution ◽  
Dynamics Simulations

The structural changes of amorphous silicon (a-Si) under compressive pressure were examined by molecular-dynamics simulations using the Tersoff interatomic potential. a-Si prepared by melt-quenching methods was pressurized up to 30 GPa under different temperatures (300K and 500K). The density of a-Si increased from 2.26 to 3.24 g/cm3 with pressure, suggesting the occurrence of the low-density to high-density amorphous phase transformation. This phase transformation occurred at the lower pressure with increasing the temperature because the activation barrier for amorphous-to-amorphous phase transformation could be exceeded by thermal energy. The coordination number increased with pressure and time, and it was saturated at different values depending on the pressure. This suggested the existence of different metastable atomic configurations in a-Si. Atomic pair-distribution functions and bond-angle distribution functions suggested that the short-range ordered structure of high-density a-Si is similar to the structure of the high-pressure phase of crystalline Si (β-tin and Imma structures).

scholarly journals SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

2019 ◽  
Vol 24 (9) ◽  
pp. 928-938 ◽  
Author(s):  
Luca Palazzolo ◽  
Chiara Paravicini ◽  
Tommaso Laurenzi ◽  
Sara Adobati ◽  
Simona Saporiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Amino Acid Residues ◽  
Dibasic Amino Acid ◽  
Novel Target ◽  
Function Relationship ◽  
Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

scholarly journals Molecular Dynamics Simulations of CO2Molecules in ZIF-11 Using Refined AMBER Force Field

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
W. Wongsinlatam ◽  
T. Remsungnen
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Distribution Functions ◽  
Binding Energies ◽  
Hydrogen Atoms ◽  
Amber Force Field ◽  
Bonding Parameters ◽  
Flexible Framework ◽  
Dynamics Simulations

Nonbonding parameters of AMBER force field have been refined based onab initiobinding energies of CO2–[C7H5N2]−complexes. The energy and geometry scaling factors are obtained to be 1.2 and 0.9 forεandσparameters, respectively. Molecular dynamics simulations of CO2molecules in rigid framework ZIF-11, have then been performed using original AMBER parameters (SIM I) and refined parameters (SIM II), respectively. The site-site radial distribution functions and the molecular distribution plots simulations indicate that all hydrogen atoms are favored binding site of CO2molecules. One slight but notable difference is that CO2molecules are mostly located around and closer to hydrogen atom of imidazolate ring in SIM II than those found in SIM I. The Zn-Zn and Zn-N RDFs in free flexible framework simulation (SIM III) show validity of adapting AMBER bonding parameters. Due to the limitations of computing resources and times in this study, the results of flexible framework simulation using refined nonbonding AMBER parameters (SIM IV) are not much different from those obtained in SIM II.

Lipid Bilayers Driven to a Wrong Lane in Molecular Dynamics Simulations by Subtle Changes in Long-Range Electrostatic Interactions

2004 ◽  
Vol 108 (14) ◽  
pp. 4485-4494 ◽  
Author(s):  
Michael Patra ◽  
Mikko Karttunen ◽  
Marja T. Hyvönen ◽  
Emma Falck ◽  
Ilpo Vattulainen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Bilayers ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Dynamics Simulations

scholarly journals 2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization

2017 ◽  
Vol 13 ◽  
pp. 1498-1506 ◽  
Author(s):  
Julia Kinzel ◽  
Daniel F Sauer ◽  
Marco Bocola ◽  
Marcus Arlt ◽  
Tayebeh Mirzaei Garakani ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Sodium Dodecyl Sulfate ◽  
Transmembrane Protein ◽  
Aqueous Media ◽  
Sodium Dodecyl ◽  
Transmembrane Proteins ◽  
Fold Increase ◽  
Hybrid Catalyst ◽  
Molecular Weights ◽  
Dynamics Simulations

Covering hydrophobic regions with stabilization agents to solubilize purified transmembrane proteins is crucial for their application in aqueous media. The small molecule 2-methyl-2,4-pentanediol (MPD) was used to stabilize the transmembrane proteinFerric hydroxamate uptake protein component A(FhuA) utilized as host for the construction of a rhodium-based biohybrid catalyst. Unlike commonly used detergents such as sodium dodecyl sulfate or polyethylene polyethyleneglycol, MPD does not form micelles in solution. Molecular dynamics simulations revealed the effect and position of stabilizing MPD molecules. The advantage of the amphiphilic MPD over micelle-forming detergents is demonstrated in the polymerization of phenylacetylene, showing a ten-fold increase in yield and increased molecular weights.

scholarly journals Collaborative Behavior of Urea and KI in Denaturing Protein Native Structure

2019 ◽  
Author(s):  
Qiang Shao ◽  
Jinan Wang ◽  
Weiliang Zhu
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Structural Dynamics ◽  
Electrostatic Interactions ◽  
Side Chain ◽  
Mixed Solution ◽  
Native Structure ◽  
Indirect Influence ◽  
Collaborative Behavior ◽  
Dynamics Simulations

AbstractIn this work, the combined influence of urea and KI on protein native structure is quantitatively investigated through the comparative molecular dynamics simulations on the structural dynamics of a polypeptide of TRPZIP4 in a series of urea/KI mixed solutions (urea concentration: 4M, KI salt concentration: 0M-6M). The observed enhanced denaturing ability of urea/KI mixture can be explained by direct interactions of urea/K+/water towards protein (electrostatic and vdW interactions from urea and electrostatic interactions from K+ and water) and indirect influence of KI on the strengthened interaction of urea towards protein backbone and side-chain. The latter indirect influence is fulfilled through the weakening of hydrogen bonding network among urea and water by the appearance of K+–water and I—urea interactions. As a result, the denaturing ability enhancement of urea and KI mixed solution is induced by the collaborative behavior of urea and KI salt.

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