scholarly journals A quantum mechanical polarizable force field for biomolecular interactions

2005 ◽  
Vol 102 (22) ◽  
pp. 7829-7834 ◽  
Author(s):  
A. G. Donchev ◽  
V. D. Ozrin ◽  
M. V. Subbotin ◽  
O. V. Tarasov ◽  
V. I. Tarasov
Keyword(s):  
Force Field ◽  
Biomolecular Interactions ◽  
Quantum Mechanical ◽  
Polarizable Force Field

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.

scholarly journals Water properties from first principles: Simulations by a general-purpose quantum mechanical polarizable force field

2006 ◽  
Vol 103 (23) ◽  
pp. 8613-8617 ◽  
Author(s):  
A. G. Donchev ◽  
N. G. Galkin ◽  
A. A. Illarionov ◽  
O. V. Khoruzhii ◽  
M. A. Olevanov ◽  
...  
Keyword(s):  
Force Field ◽  
First Principles ◽  
General Purpose ◽  
Quantum Mechanical ◽  
Polarizable Force Field ◽  
Water Properties

Testing and Optimizing the Drude Polarizable Force Field for Blocked Amino Acids Based on High-Level Quantum-Mechanical Energy Surfaces

2022 ◽  
pp. 1-9
Author(s):  
Jinfeng Chen ◽  
Gerhard König
Keyword(s):  
Amino Acids ◽  
Force Field ◽  
Energy Surface ◽  
Mechanical Energy ◽  
Quantum Mechanical ◽  
Polarizable Force Field ◽  
Conformational Substates ◽  
Reorganization Energies ◽  
High Level ◽  
Energy Surfaces

The correct reproduction of conformational substates of amino acids was tested for the CHARMM Drude polarizable force field. This was achieved by evaluating the reorganization energies for all low lying energy minima occurring in all 15 neutral blocked amino acids on a quantum-mechanical (QM) energy surface at the MP2/cc-pVDZ level. The results indicate that the bonded parameters of the N-acetyl (ACE) and N-Methylamide (CT3) blocking groups lead to significant discrepancies. A reparametrization of five bond angles significantly improved the agreement with the QM energy surface. The corrected Drude force field exhibits almost the same average reorganization energies relative to the MP2 energy surface as the AM1 and PM3 semi-empirical methods.

Modelling Flexible Protein-Ligand Binding in p38α MAP Kinase using the QUBE Force Field

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Map Kinase ◽  
Binding Free Energy ◽  
Quantum Mechanical ◽  
Enhanced Sampling ◽  
Relative Binding ◽  
Stringent Test ◽  
Flexible Protein ◽  
P38α Map Kinase

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field is used to retrospectively calculate the relative binding free energy of a series of 17 flexible inhibitors of p38α MAP kinase. The size and flexibility of the chosen molecules represent a stringent test of the derivation of force field parameters from quantum mechanics, and enhanced sampling is required to reduce the dependence of the results on the starting structure. Competitive accuracy with a widely-used biological force field is achieved, indicating that quantum mechanics derived force fields are approaching the accuracy required to provide guidance in prospective drug discovery campaigns.</p></div></div></div>

Sign in / Sign up

Export Citation Format

Share Document