Molecular dynamics investigation of water-exchange reactions on lanthanide ions in water/1-ethyl-3-methylimidazolium trifluoromethylsufate ([EMIm][OTf])

2018 ◽  
Vol 148 (2) ◽  
pp. 024503 ◽  
Author(s):  
Yi-Jung Tu ◽  
Zhijin Lin ◽  
Matthew J. Allen ◽  
G. Andrés Cisneros
Keyword(s):  
Molecular Dynamics ◽  
Water Exchange ◽  
Lanthanide Ions ◽  
Exchange Reactions

Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

2016 ◽  
Vol 18 (44) ◽  
pp. 30323-30333 ◽  
Author(s):  
Yi-Jung Tu ◽  
Matthew J. Allen ◽  
G. Andrés Cisneros
Keyword(s):  
Molecular Dynamics ◽  
Exchange Rates ◽  
Molecular Dynamics Simulations ◽  
Water Exchange ◽  
Experimental Results ◽  
Lanthanide Ions ◽  
Ethyl Sulfate ◽  
Dynamics Simulations

Molecular dynamics simulations have been carried out to explain the water-exchange rates of lanthanide ions in water and water/[EMIm][EtSO4] observed from 17O-NMR experiments. Our simulations are in agreement with experimental results with respect to water-exchange trends.

scholarly journals Current Status of AMOEBA–IL: A Multipolar/Polarizable Force Field for Ionic Liquids

2020 ◽  
Vol 21 (3) ◽  
pp. 697
Author(s):  
Erik Antonio Vázquez-Montelongo ◽  
José Enrique Vázquez-Cervantes ◽  
G. Andrés Cisneros
Keyword(s):  
Ionic Liquid ◽  
Force Field ◽  
Decomposition Analysis ◽  
Lanthanide Ions ◽  
Current Status ◽  
Energy Decomposition Analysis ◽  
Quantum Mechanical ◽  
Exchange Reactions ◽  
Polarizable Force Field ◽  
Liquid Systems

Computational simulations of ionic liquid solutions have become a useful tool to investigate various physical, chemical and catalytic properties of systems involving these solvents. Classical molecular dynamics and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of IL systems have provided significant insights at the atomic level. Here, we present a review of the development and application of the multipolar and polarizable force field AMOEBA for ionic liquid systems, termed AMOEBA–IL. The parametrization approach for AMOEBA–IL relies on the reproduction of total quantum mechanical (QM) intermolecular interaction energies and QM energy decomposition analysis. This approach has been used to develop parameters for imidazolium– and pyrrolidinium–based ILs coupled with various inorganic anions. AMOEBA–IL has been used to investigate and predict the properties of a variety of systems including neat ILs and IL mixtures, water exchange reactions on lanthanide ions in IL mixtures, IL–based liquid–liquid extraction, and effects of ILs on an aniline protection reaction.

Interpretation of Activation Volumes for Water Exchange Reactions Revisited: AbInitioCalculations for Al3+, Ga3+, and In3+, and New Experimental Data

1998 ◽  
Vol 120 (26) ◽  
pp. 6569-6577 ◽  
Author(s):  
Th. Kowall ◽  
P. Caravan ◽  
H. Bourgeois ◽  
L. Helm ◽  
F. P. Rotzinger ◽  
...  
Keyword(s):  
Experimental Data ◽  
Water Exchange ◽  
Exchange Reactions

scholarly journals A molecular dynamics study of bond exchange reactions in covalent adaptable networks

Soft Matter ◽  
2015 ◽  
Vol 11 (31) ◽  
pp. 6305-6317 ◽  
Author(s):  
Hua Yang ◽  
Kai Yu ◽  
Xiaoming Mu ◽  
Xinghua Shi ◽  
Yujie Wei ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Exchange Reactions ◽  
Network Polymers ◽  
Active Unit

A molecular dynamics approach is used to study the network rearrangement in covalent adaptable network polymers through bond exchange reactions where an active unit attaches to an existing bond then kicks off its pre-existing peer to form a new bond.

Multiple Steering Molecular Dynamics Applied to Water Exchange at Alkali Ions

2002 ◽  
Vol 106 (50) ◽  
pp. 13027-13032 ◽  
Author(s):  
Michele Cascella ◽  
Leonardo Guidoni ◽  
Amos Maritan ◽  
Ursula Rothlisberger ◽  
Paolo Carloni
Keyword(s):  
Molecular Dynamics ◽  
Water Exchange ◽  
Alkali Ions

scholarly journals Enhancing Water Sampling of Buried Binding Sites Using Nonequilibrium Candidate Monte Carlo

2020 ◽  
Author(s):  
Teresa Danielle Bergazin ◽  
Ido Ben-Shalom ◽  
Nathan M. Lim ◽  
Samuel C. Gill ◽  
Michael K. Gilson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Binding Sites ◽  
Water Exchange ◽  
Free Energy Calculations ◽  
Water Molecules ◽  
Water Sampling ◽  
Computer Aided Drug Design ◽  
Practical Applications ◽  
Computer Aided

<div>Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our NCMC/MD method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.</div>

Sign in / Sign up

Export Citation Format

Share Document