Direct calculation of 1-octanol–water partition coefficients from adaptive biasing force molecular dynamics simulations

2012 ◽  
Vol 137 (1) ◽  
pp. 014502 ◽  
Author(s):  
Navendu Bhatnagar ◽  
Ganesh Kamath ◽  
Issac Chelst ◽  
Jeffrey J. Potoff
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Partition Coefficients ◽  
Direct Calculation ◽  
Adaptive Biasing ◽  
Dynamics Simulations ◽  
Adaptive Biasing Force

Prediction of Micelle/Water and Liposome/Water Partition Coefficients Based on Molecular Dynamics Simulations, COSMO-RS, and COSMOmic

Langmuir ◽  
2013 ◽  
Vol 29 (11) ◽  
pp. 3527-3537 ◽  
Author(s):  
Thomas Ingram ◽  
Sandra Storm ◽  
Linda Kloss ◽  
Tanja Mehling ◽  
Sven Jakobtorweihen ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Partition Coefficients ◽  
Dynamics Simulations

scholarly journals Pyranose Ring Puckering Thermodynamics for Glycan Monosaccharides Associated with Vertebrate Proteins

2021 ◽  
Vol 23 (1) ◽  
pp. 473
Author(s):  
Olgun Guvench ◽  
Devon Martin ◽  
Megan Greene
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Biomolecular Dynamics ◽  
Explicit Solvent ◽  
Conformational Properties ◽  
Adaptive Biasing ◽  
Charmm Force Field ◽  
Ring Puckering ◽  
Dynamics Simulations

The conformational properties of carbohydrates can contribute to protein structure directly through covalent conjugation in the cases of glycoproteins and proteoglycans and indirectly in the case of transmembrane proteins embedded in glycolipid-containing bilayers. However, there continue to be significant challenges associated with experimental structural biology of such carbohydrate-containing systems. All-atom explicit-solvent molecular dynamics simulations provide a direct atomic resolution view of biomolecular dynamics and thermodynamics, but the accuracy of the results depends on the quality of the force field parametrization used in the simulations. A key determinant of the conformational properties of carbohydrates is ring puckering. Here, we applied extended system adaptive biasing force (eABF) all-atom explicit-solvent molecular dynamics simulations to characterize the ring puckering thermodynamics of the ten common pyranose monosaccharides found in vertebrate biology (as represented by the CHARMM carbohydrate force field). The results, along with those for idose, demonstrate that the CHARMM force field reliably models ring puckering across this diverse set of molecules, including accurately capturing the subtle balance between 4C1 and 1C4 chair conformations in the cases of iduronate and of idose. This suggests the broad applicability of the force field for accurate modeling of carbohydrate-containing vertebrate biomolecules such as glycoproteins, proteoglycans, and glycolipids.

Molecular Dynamics Simulations of Carbon Nanotube Interactions in Water/Surfactant Systems

2010 ◽  
Vol 132 (2) ◽  
Author(s):  
Nasir M. Uddin ◽  
Franco Capaldi ◽  
Bakhtier Farouk
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Potential Of Mean Force ◽  
Quantitative Prediction ◽  
The Matrix ◽  
Adaptive Biasing ◽  
Speed Up ◽  
Dynamics Simulations ◽  
Processing Techniques ◽  
Walled Carbon Nanotubes

The properties of nanocomposite materials depend on the dispersion of the nanoparticles/nanofibers within the matrix. The addition of surfactants and varied processing techniques are used to increase the dispersion of the nanoparticles in the final composite. A method for the quantitative prediction of the interactions between nanoparticles in solution would aid in the design of processing schedules. In this study, molecular dynamics simulations are used to compute for the potential of mean force as a function of the distance and orientation between a pair of single-walled carbon nanotubes (CNTs) in water. An adaptive biasing force method is used to speed up the calculations. Simulation results show that CNT orientation and the addition of surfactant can significantly affect CNT interactions and inturn dispersion.

Solvent-dependent conformation of cyclosporin a: evidence from partition coefficients and molecular dynamics simulations

1993 ◽  
Vol 11 (4) ◽  
pp. 260-261
Author(s):  
NabilEl Tayar ◽  
AlanE. Mark ◽  
Philippe Vallat ◽  
RogerM. Brunne ◽  
Bernard Testa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Cyclosporin A ◽  
Molecular Dynamics Simulations ◽  
Partition Coefficients ◽  
Dynamics Simulations
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