Molecular Modelling of Small Molecule Diffusion in Biopolymer Blends Membranes for Biomedical Applications

2006 ◽  
Author(s):  
Mariana Ionita ◽  
Davide Silvestri ◽  
Alfonso Gautieri ◽  
Emiliano Votta ◽  
Gianluca Ciardelli ◽  
...  
Keyword(s):  
Small Molecules ◽  
Diffusion Coefficients ◽  
Diffusion Constant ◽  
Polymeric Materials ◽  
Md Simulations ◽  
Synthetic Polymers ◽  
Computational Method ◽  
Poly Vinyl Alcohol ◽  
Dynamics Simulations ◽  
Biological Performance

In order to improve the biological performance of synthetic polymers and to enhance the mechanical characteristics by tailoring the permeability properties of biopolymers, a new class of specifically designed materials (bioartificial polymeric materials), consisting of blends of synthetic polymers and biopolymers, has been recently introduced. In this work we present a computational method based on molecular mechanics (MM) and dynamics (MD) techniques, to investigate their permeability to small molecules. The permeability properties was assessed of poly(vinyl alcohol)-(PVA)- dextran-(Dex) and poly(acrylic acid)-(PAA)-Dex membranes with different blend composition. Amorphous bulk models of PVA–Dex and PAA–Dex mixtures with 80:20, 60:40, 40:60 (w/w) ratios were generated. Two steps have been performed iteratively, the former using a MM simulation for equilibration and the latter using MD simulations for model refinement. Virtual uniaxial traction tests were performed, adopting the Second Derivative (SD) procedure, in order to assess the mechanical behavior of the bulk models. The diffusion coefficients for H2O were determined via NVT molecular dynamics simulations. Using the data of the motion of water inside the bulk models, the diffusivity constant was calculated applying the Einstein equation. Correlation of diffusion coefficients with free volume, was found. The results of the simulations agree with theoretical considerations: as the content of dextran increases from 80:20 to 40:60 a 86 % decrease of the diffusion constant is obtained and the values (range 0.14–56.5 10−6 cm2s−1) have the order of magnitude expected, and similar on the diffusion of small molecules in amorphous polymeric membranes.

Predicting Methane Diffusivity in Polymeric Membranes by Molecular Dynamics

2015 ◽  
Vol 1119 ◽  
pp. 461-465
Author(s):  
M.K. Hadj-Kali ◽  
A. Bessadok-Jemai ◽  
S. Haider ◽  
Y. Alzeghayer
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Polymeric Membranes ◽  
Transport Mechanisms ◽  
Fluid Equation ◽  
Cell Modules ◽  
Dynamics Simulations ◽  
Materials Studio

Diffusion coefficients of methane (CH4) have been obtained by Molecular Dynamics (MD) simulations combined with Einstein fluid equation. Three polymers were considered, namely polyethylene, polypropylene and poly (cis-1,4-butadiene). All calculations were performed by means of Polymer Builder and Amorphous Cell modules within Materials Studio (Accelrys). The obtained diffusivity results are within the range of published results for similar small molecules. Molecular dynamics simulations proved to be a useful tool for understanding the detailed descriptions and transport mechanisms occurring within the material.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

scholarly journals All-Atom MD Simulations of the HBV Capsid Complexed with AT130 Reveal Secondary and Tertiary Structural Changes and Mechanisms of Allostery

2021 ◽  
Author(s):  
Carolina Pérez Segura ◽  
Boon Chong Goh ◽  
Jodi A. Hadden-Perilla
Keyword(s):  
Small Molecules ◽  
Drug Target ◽  
Structural Changes ◽  
Salt Bridge ◽  
Md Simulations ◽  
Health Concern ◽  
Protein Dimer ◽  
B Virus ◽  
Flexible Protein ◽  
Dynamics Simulations

AbstractThe hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important anti-viral paradigm based on disrupting the timing of genome encapsulation. Crystallographic studies of AT130-bound complexes have been essential in explaining the effects of the small molecule on HBV capsid structure; however, computational examination reveals that key changes attributed to AT130 were erroneous, likely a consequence of interpreting poor resolution arising from a highly flexible protein. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that, rather than damaging spike helicity, AT130 enhances the capsid’s ability to recover it. A new conformational state is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these domains. Combined with dynamical network analysis, results describe a connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire capsid protein dimer.

Molecular Dynamics Simulations of Atoms Diffusion in Solid

2018 ◽  
Vol 15 ◽  
pp. 51-64
Author(s):  
Yu Lu Zhou ◽  
Xiao Ma Tao ◽  
Qing Hou ◽  
Yi Fang Ouyang
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Einstein Relation ◽  
Interatomic Potentials ◽  
Body System ◽  
Many Body ◽  
Point Particles ◽  
Bulk Surface ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations, which treat atoms as point particles and trace their individual trajectories, are always employed to investigate the transport properties of a many-body system. The diffusion coefficients of atoms in solid can be obtained by the Einstein relation and the Green-Kubo relation. An overview of the MD simulations of atoms diffusion in the bulk, surface and grain boundary is provided. We also give an example of the diffusion of helium in tungsten to illustrate the procedure, as well as the importance of the choice of interatomic potentials. MD simulations can provide intuitive insights into the atomic mechanisms of diffusion.

Study of the Hydrogen Bond Network in sub-and supercritical Water by Molecular Dynamics Simulations

2001 ◽  
Vol 56 (8) ◽  
pp. 579-584 ◽  
Author(s):  
S. Krishtal ◽  
M. Kiselev ◽  
Y. Puhovski ◽  
T. Kerdcharoen ◽  
S. Hannongbua ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Critical Point ◽  
Supercritical Water ◽  
Diffusion Coefficients ◽  
Md Simulations ◽  
Saturation Curve ◽  
Hydrogen Bond Network ◽  
Self Diffusion ◽  
Bond Network ◽  
Dynamics Simulations

Abstract For 12 points along the tangent to the saturation curve at the critical point the temperature dependen­cies of the heights of the first maximum in the 0 -0 RDF, the average number of hydrogen bonds, and the self-diffusion coefficients have been calculated from MD simulations. The curves of these three properties show an inflection near the critical point. To improve the understanding of these changes in going from subcritical to supercritical water the librational spectra and the change in the fractions of wa­ter molecules with a given number of hydrogen bonds as a function of temperature have been derived from the simulations, additionally.

Lanthanoids(III) and actinoids(III) in water: Diffusion coefficients and hydration enthalpies from polarizable molecular dynamics simulations

2012 ◽  
Vol 85 (1) ◽  
pp. 237-246 ◽  
Author(s):  
Fausto Martelli ◽  
Sacha Abadie ◽  
Jean-Pierre Simonin ◽  
Rodolphe Vuilleumier ◽  
Riccardo Spezia
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Heavy Ions ◽  
Md Simulations ◽  
Contradictory Result ◽  
Dielectric Friction ◽  
Water Interaction ◽  
Diffusive Regime ◽  
Dynamics Simulations ◽  
Good Agreement

By using polarizable molecular dynamics (MD) simulations of lanthanoid(III) and actinoid(III) ions in water, we obtained ionic diffusion coefficients and hydration enthalpies for both series. These values are in good agreement with experiments. Simulations thus allow us to relate them to microscopic structure. In particular, across the series the diffusion coefficients decrease, reflecting the increase of ion–water interaction. Hydration enthalpies also show that interactions increase from light to heavy ions in agreement with experiment. The apparent contradictory result of the decrease of the diffusion coefficient with decreasing ionic radius is tentatively explained in terms of dielectric friction predominance on Stokes’ diffusive regime.

scholarly journals Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.

2003 ◽  
Vol 50 (3) ◽  
pp. 789-798 ◽  
Author(s):  
Tomasz Róg ◽  
Krzysztof Murzyn ◽  
Marta Pasenkiewicz-Gierula
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Md Simulations ◽  
Computational Method ◽  
Simulation Protocol ◽  
Speed Up ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations complement experimental methods in studies of the structure and dynamics of lipid bilayers. The choice of algorithms employed in this computational method represents a trade-off between the accuracy and real calculation time. The largest portion of the simulation time is devoted to calculation of long-range electrostatic interactions. To speed-up evaluation of these interactions, various approximations have been used. The most common ones are the truncation of long-range interactions with the use of cut-offs, and the particle-mesh Ewald (PME) method. In this study, several multi-nanosecond cut-off and PME simulations were performed to establish the influence of the simulation protocol on the bilayer properties. Two bilayers were used. One consisted of neutral phosphatidylcholine molecules. The other was a mixed lipid bilayer consisting of neutral phosphatidylethanolamine and negatively charged phosphatidylglycerol molecules. The study shows that the cut-off simulation of a bilayer containing charge molecules generates artefacts; in particular the mobility and order of the charged molecules are vastly different from those determined experimentally. In the PME simulation, the bilayer properties are in general agreement with experimental data. The cut-off simulation of bilayers containing only uncharged molecules does not generate artefacts, nevertheless, the PME simulation gives generally better agreement with experimental data.

Molecular iodine/polymer complexes

2013 ◽  
Vol 33 (5) ◽  
pp. 389-443 ◽  
Author(s):  
Saad Moulay
Keyword(s):  
Polymeric Materials ◽  
Molecular Iodine ◽  
Synthetic Polymers ◽  
Vinyl Pyrrolidone ◽  
Poly Vinyl Alcohol ◽  
Polymer Complex ◽  
Natural Polymers ◽  
Polymer Complexes ◽  
Conductivity Enhancement ◽  
Unexpected Findings

Abstract A unique feature of molecular iodine by far, is its ability to bind to polymeric materials. A plethora of natural and synthetic polymers develop complexes when treated with molecular iodine, or with a mixture of molecular iodine and potassium iodide. Many unexpected findings have been encountered upon complexation of iodine and the polymer skeleton, including the color formation, the polymer morphology changes, the complexation sites or regions, the biological activity, and the electrical conductivity enhancement of the complexes, with polyiodides (In¯), mainly I3¯ and I5¯, as the actual binding species. Natural polymers that afford such complexes with iodine species are starch (amylose and amylopectin), chitosan, glycogen, silk, wool, albumin, cellulose, xylan, and natural rubber; iodine-starch being the oldest iodine-natural polymer complex. By contrast, numerous synthetic polymers are prone to make complexes, including poly(vinyl alcohol) (PVA), poly(vinyl pyrrolidone) (PVP), nylons, poly(Schiff base)s, polyaniline, unsaturated polyhydrocarbons (carbon nanotubes, fullerenes C60/C70, polyacetylene; iodine-PVA being the oldest iodine-synthetic polymer complex.

A Molecular Modelling Approach for Designing Bioartificial Membranes for Clinical Use With Tailored Transport Properties

2007 ◽  
Author(s):  
Mariana Ionita ◽  
Alfonso Gautieri ◽  
Emiliano Votta ◽  
Alberto Redaelli
Keyword(s):  
Mechanical Properties ◽  
Acrylic Acid ◽  
Small Molecules ◽  
Experimental Studies ◽  
Computational Method ◽  
Poly Vinyl Alcohol ◽  
Clinical Use ◽  
And Diffusion ◽  
Modelling Approach ◽  
Diffusion Properties

There has been a demand for hemodialysis membranes with better biocompatibility, the use of which would reduce the incidence of complications in patients who have been under long hemodialysis treatment. Recently, highly biocompatible membranes have been obtained by blending synthetic and polymers [1]. Specifically, poly(vinyl-alcohol) (PVA) and poly(acrylic acid) (PAA) have been combined with chitosan (Chi) and dextran (Dex) to create a biomaterials with excellent biocompatibility and mechanical properties. In this work we present a computational method based on molecular mechanics (MM) and dynamics (MD) techniques have been combined with an experimental studies, with the aim of designing and forecasting the permeability and diffusion properties of these membranes to small molecules, as a function of their composition.

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

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