Enantioselective Palladium-Catalyzed Hydrosilylation of Styrene:  Influence of Electronic and Steric Effects on Enantioselectivity and Catalyst Design via Hybrid QM/MM Molecular Dynamics Simulations

2006 ◽  
Vol 25 (5) ◽  
pp. 1151-1157 ◽  
Author(s):  
Alessandra Magistrato ◽  
Antonio Togni ◽  
Ursula Rothlisberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Catalyst Design ◽  
Steric Effects ◽  
Palladium Catalyzed ◽  
Dynamics Simulations ◽  
Electronic And Steric Effects

scholarly journals Reactive modeling of the initial stages of alkoxysilane polycondensation: effects of precursor molecule structure and solution composition

Soft Matter ◽  
2015 ◽  
Vol 11 (34) ◽  
pp. 6780-6789 ◽  
Author(s):  
Joshua D. Deetz ◽  
Roland Faller
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Steric Effects ◽  
Solution Composition ◽  
Precursor Molecule ◽  
Molecule Structure ◽  
Reactive Molecular Dynamics ◽  
Water Composition ◽  
Dynamics Simulations ◽  
The Impact

Reactive molecular dynamics simulations are used to model polycondensation of alkoxysilanes in solution. Different precursor monomers are compared and steric effects on polycondensation kinetics are observed. The impact of the alcohol and water composition in solution are explored.

scholarly journals Ion-triggered selectivity in bacterial sodium channels

2018 ◽  
Vol 115 (21) ◽  
pp. 5450-5455 ◽  
Author(s):  
Simone Furini ◽  
Carmen Domene
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Hydration Shell ◽  
Membrane Potentials ◽  
Free Energy Calculations ◽  
Selectivity Filter ◽  
Atomic Scale ◽  
Steric Effects ◽  
Potassium Ions ◽  
Dynamics Simulations

Since the availability of the first crystal structure of a bacterial Na+ channel in 2011, understanding selectivity across this family of membrane proteins has been the subject of intense research efforts. Initially, free energy calculations based on molecular dynamics simulations revealed that although sodium ions can easily permeate the channel with their first hydration shell almost intact, the selectivity filter is too narrow for efficient conduction of hydrated potassium ions. This steric view of selectivity was subsequently questioned by microsecond atomic trajectories, which proved that the selectivity filter appears to the permeating ions as a highly degenerate, liquid-like environment. Although this liquid-like environment looks optimal for rapid conduction of Na+, it seems incompatible with efficient discrimination between similar ion species, such as Na+ and K+, through steric effects. Here extensive molecular dynamics simulations, combined with Markov state model analyses, reveal that at positive membrane potentials, potassium ions trigger a conformational change of the selectivity toward a nonconductive metastable state. It is this transition of the selectivity filter, and not steric effects, that prevents the outward flux of K+ at positive membrane potentials. This description of selectivity, triggered by the nature of the permeating ions, might have implications on the current understanding of how ion channels, and in particular bacterial Na+ channels, operate at the atomic scale.

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