Molecular dynamics simulations and experimental studies of the formation of endohedral complexes of buckminsterfullerene

1992 ◽  
Vol 96 (12) ◽  
pp. 4755-4761 ◽  
Author(s):  
R. C. Mowrey ◽  
M. M. Ross ◽  
J. H. Callahan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Endohedral Complexes ◽  
Dynamics Simulations

scholarly journals Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Renu Wadhwa ◽  
Neetu Singh Yadav ◽  
Shashank P. Katiyar ◽  
Tomoko Yaguchi ◽  
Chohee Lee ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cell Membrane ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Bilayer Membrane ◽  
Withaferin A ◽  
Head Group ◽  
Polar Head Group ◽  
Natural Drugs ◽  
Dynamics Simulations

AbstractPoor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs—withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.

scholarly journals Nanoformulation-by-design: an experimental and molecular dynamics study for polymer coated drug nanoparticles

RSC Advances ◽  
2020 ◽  
Vol 10 (33) ◽  
pp. 19521-19533 ◽  
Author(s):  
Ioanna Danai Styliari ◽  
Vincenzo Taresco ◽  
Andrew Theophilus ◽  
Cameron Alexander ◽  
Martin Garnett ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
High Drug ◽  
Nanoparticle Formation ◽  
Polymer Nanoparticle ◽  
Drug Nanoparticles ◽  
Dynamics Simulations

Experimental studies of drug–polymer nanoparticle formation combined with molecular dynamics simulations provide atomistic explanations for the high drug loadings obtained.

Experimental Studies and Molecular Dynamics Simulations of the Sliding Contact of Metallic Glass

2000 ◽  
Vol 644 ◽  
Author(s):  
Xi-Yong Fu ◽  
Michael L. Falk ◽  
David A. Rigney
Keyword(s):  
Molecular Dynamics ◽  
Metallic Glass ◽  
Molecular Dynamics Simulations ◽  
Bulk Metallic Glass ◽  
Amorphous Material ◽  
Experimental Studies ◽  
Sliding Contact ◽  
Atomic Scale ◽  
Sliding Interface ◽  
Dynamics Simulations

AbstractTribological properties of bulk metallic glass Zr41.2Ti13.8Cu12.5Ni10.0Be22.5 were studied experimentally using a pin/disk geometry without lubrication. Experimental observations were compared with 2D molecular dynamics simulations of amorphous material in sliding contact. The friction coefficient and the wear rate of bulk metallic glass (BMG) depend on normal load and test environment. The sliding of annealed BMG re-amorphizes devitrified material. A mechanically mixed layer is generated during sliding; this layer has enhanced oxygen content if the sliding is in air. The MD simulations show that atomic scale mixing occurs across the sliding interface. The growth kinetics of the mixing process scales with the square root of time. In the simulations, a low density region is generated near the sliding interface; it corresponds spatially to the softer layer detected in experiments. Subsurface displacement profiles produced by sliding and by simulation are very similar and are consistent with the flow patterns expected from a simple Navier-Stokes analysis when the stress state involves both compression and shear.

Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides

2016 ◽  
Vol 138 (20) ◽  
pp. 6532-6540 ◽  
Author(s):  
Stacy L. Chin ◽  
Qing Lu ◽  
Eric L. Dane ◽  
Laura Dominguez ◽  
Christopher J. McKnight ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Structure And Dynamics ◽  
Dynamics Simulations

scholarly journals Coarse-grained molecular dynamics simulations reveal lipid access pathways in P-glycoprotein

2018 ◽  
Vol 150 (3) ◽  
pp. 417-429 ◽  
Author(s):  
Estefania Barreto-Ojeda ◽  
Valentina Corradi ◽  
Ruo-Xu Gu ◽  
D. Peter Tieleman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Experimental Studies ◽  
Lipid Binding ◽  
Coarse Grained ◽  
Glycoprotein P ◽  
P Glycoprotein ◽  
Dynamics Simulations ◽  
Positively Charged ◽  
Coarse Grained Molecular Dynamics

P-glycoprotein (P-gp) exports a broad range of dissimilar compounds, including drugs, lipids, and lipid-like molecules. Because of its substrate promiscuity, P-gp is a key player in the development of cancer multidrug resistance. Although P-gp is one of the most studied ABC transporters, the mechanism by which its substrates access the cavity remains unclear. In this study, we perform coarse-grained molecular dynamics simulations to explore possible lipid access pathways in the inward-facing conformation of P-gp embedded in bilayers of different lipid compositions. In the inward-facing orientation, only lipids from the lower leaflet access the cavity of the transporter. We identify positively charged residues at the portals of P-gp that favor lipid entrance to the cavity, as well as lipid-binding sites at the portals and within the cavity, which is in good agreement with previous experimental studies. This work includes several examples of lipid pathways for phosphatidylcholine and phosphatidylethanolamine lipids that help elucidate the molecular mechanism of lipid binding in P-gp.

scholarly journals Learning to Model G-Quadruplexes: Current Methods and Perspectives

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Iker Ortiz de Luzuriaga ◽  
Xabier Lopez ◽  
Adrià Gil3
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Density Functional ◽  
Experimental Studies ◽  
Annual Review ◽  
Publication Date ◽  
Square Planar ◽  
Explicit Simulation ◽  
Dynamics Simulations

G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into two main categories: ( a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and ( b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Effect of conductivity, viscosity, and density of water-in-salt electrolytes on the electrochemical behavior of supercapacitors: molecular dynamics simulations and in-situ characterization studies.

2021 ◽  
Author(s):  
Débora Ariana Corrêa da Silva ◽  
Manuel Jonathan Pinzón ◽  
Andresa Messias ◽  
Eudes E. Fileti ◽  
Aline Pascon ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrochemical Behavior ◽  
Experimental Studies ◽  
In Situ Characterization ◽  
Advantages And Disadvantages ◽  
Characterization Studies ◽  
Dynamics Simulations ◽  
Density Of Water

It is reported the combination of molecular dynamics simulations and different experimental studies to understand the advantages and disadvantages of departing from conventional (salt-in-water,SiWE) aqueous-based electrolytes to very concentrated (water-in-salt,...

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