Chemistry Reference
In-Depth Information
There is a wide range of solvation methods with varying sophistication, accuracy,
computational cost and usage of implicit solvents. Explicit solvation incorporated
in the molecular dynamics free energy perturbation (FEP/MD) which includes
explicit solvent molecules in order to provide a realistic treatment of solvation
with computational cost limitations. Some methods use mixed explicit/implicit
solvent schemes. Other combination methods include quantum mechanics/free
energy perturbation (QM/FEP), grand canonical Monte Carlo/Molecular
Dynamics (GCMD/MD) schemes [580].
Multi-copy methods (MCM) places and minimizes many small molecule probes
on the protein's surface in order to define the most important interactions.
Multicopy simultaneous search (MCSS) is used to retain only the lowest-energy
probes [581].
The continuum mean-field model describes electrostatic and non-electrostatic
interactions between a molecule and the surrounding medium. The model
combined with Hartree-Fock theory or density functional theory is used to
describe the self-consistent-field polarization of the solute's electronic structure
by a solvent [582].
It was recently presented a revised version of the water many-body problem
denoted TCPE/2013, This is based on a static three charge sites and a single
polarizable site, The protocol models the molecular electrostatic properties of
water. Considering anisotropic short ranges, there is designed a many-body
energy term to accurately model hydrogen bonding in water. The parameters
involved reproduce, up to hexamers, the
ab initio
energetic and geometrical
properties of small water clusters as well as the repulsive water interactions
occurring in cation first hydration shells. It also reproduces two liquid water
properties at ambient conditions, the density and the vaporization enthalpy. It
reproduces several important water properties. The model appears thus to be
particularly well-suited for characterizing ion hydration properties under different
temperature/pressure/phases/interfaces [371].
Recent work (2014) has emphasized the importance of water in protein
aggregation. Effectively, a currently very important problem, for treating protein-
