The Treatment of Solvent in Multiscale Biophysical Modeling

Abstract

Different approaches for treating the solvent in biophysical simulations are reviewed. They include explicit atomistic (classical fixed‐charge, polarizable, or ab initio), explicit coarse‐grained (polarizable or not), and implicit approaches (dielectric‐based or empirical). The solvent is usually an aqueous electrolyte solution, but it can also be an aqueous mixture or heterogeneous, as in micelles and lipid bilayers. The treatment of the solvent is tied to that of the solute, with implicit solvation exhibiting the highest versatility. Applications of implicit and coarse‐grained solvent modeling include a wide range of biological processes, such as protein folding, ligand binding, lipid self‐assembly, and transmembrane translocation. The advantages and disadvantages of each approach are discussed and thoughts are offered on the optimal choice of method for different problems.

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

“…[2][3][4][5] In the simplest CG water model, one represents each water molecule with a single site. [6][7][8] However, there is even greater gain when multiple (typically [3][4][5] water molecules are modeled as a single site model. The most used CG water model of this kind is the one developed by Marrink et al in the MARTINI force field.…”

Unraveling the Intrinsic Color of Chlorophyll

“…From their absorption spectra, it is evident that the molecules strongly absorb light in the red and blue regions of the visible spectrum (the Q and Soret bands, respectively), which in the absence of strongly colored secondary pigments is responsible for the green color of plant leaves. [5][6][7] Despite many developments in this field, excited-state calculations where some attempt is made to include such effects still inevitably possess a greater degree of uncertainty. The absorption spectra in ether solution display a difference of 232 nm between the Q band and Soret band maxima for Chl a whilst this is reduced to 189 nm for Chl b by a blue-shift of the Q band and red-shift of the Soret band.…”

“…[4] Spectra of Chls dissolved in different solvents are abundant, but to make a rigorous comparison between experiment and theory, a more complete treatment of solvent effects in electronic structure calculations is needed. [5][6][7] Despite many developments in this field, excited-state calculations where some attempt is made to include such effects still inevitably possess a greater degree of uncertainty. [8][9][10] It should also be borne in mind that the natural photosynthetic environment of a Chl molecule is usually a protein pocket, which is not necessarily well-modeled by bulk solvent.…”

Non-conformal coarse-grained potentials for water

“…The general goal of coarsegraining is to reduce the number of degrees of freedom allowing for significantly longer simulation times and larger systems yet retaining the essential physical properties [16][17][18] . There is no single approach to coarsegraining and a large number of CG models with unique strengths and weaknesses exist [16][17][18][19] . Apart from implicit solvent models, each of the approaches has their own model(s) for water [19][20][21] .…”