DETERMINACIÓN DE LA CONCENTRACIÓN INICIAL DEL PRECURSOR

The Martini force field developed by Siewert-Jan Marrink and co-workers eschews sys- tematic structure-matching in pursuit of a maximally transferable force field which is parameterized in a “top-down” manner, designed to encode information about the free energy of the chemical components, thereby increasing the range of thermody- namic ensembles over which the model is valid. To date, it has been used to study a broad range of biological soft-matter systems described in sections 2.2.5, 2.3.2, and 2.4.

The Martini model employs a four-to-one mapping of water and non-hydrogen atoms onto a single a bead, except in ring-like structures, which preserve geometry with a finer mapping. Molecules are built from relatively few bead types which are categorized by polarity (polar, non-polar, apolar, and charged). Each type is further distinguished by hydrogen bonding capabilities (donor, acceptor, both, or none) as well as a score describing the level of polarity. Like the CMM-CG and MS-CG models, Lennard-Jones parameters for non-bonded interactions are tuned for each pair of particles. These potentials are shifted to mimic a distance-dependent screening effect, and increase computational efficiency. Charged groups interact via a Coulomb potential Uelec(r) = _4πqi₀qj_rr with a low relative dielectric of (r = 15) for

explicit screening. This allows the use of full charges while reproducing salt structure factors seen in previous atomistic studies [212] as well as the hydration shell identified by neutron diffraction studies [63]. Non-bonded interactions for all bead types are tuned to semi-quantitatively match basic measurements of density and compressibility [187].

Bonded interactions are specified by potential energy functions which model bonds, angles, dihedrals, and impropers with harmonic functions, with relatively weak force constants to match flexibility of target molecules at the fine-grained resolutions.

Vb = 1 2Kb(dij −db) 2_(bond) Va = 1

2Ka(cos(φijk)−cos(φa))

2_(angle)

Vd = Kd(1 + cos(θijkl−θd))2(dihedral)

Vid = Kid(θijkl−θid)2(improper dihedral)

Here V represents the component of the potential energy function arising from bond, angle, dihedral, and improper dihedral contributions, the set {Kb,Ka,Kd,Kid}

represents the corresponding stiffness constants, and the set {db, φa, θd, θid} repre-

sents the equilibrium values for these interactions. Dihedral potentials are only im- plemented for peptide backbones. Alkanes are constructed to reproduce dihedral, bond, and angle parameters given by atomistic simulations in the GROMOS force field [59]. Simulations of small ice cubes surrounded by water show that Martini ice is in equilibrium with liquid water at 290K and melts within 5K of this temperature. Like many CG models, Martini water becomes supercooled as the temperature is lowered, failing to freeze spontaneously until 240K [210].

The defining feature of the Martini force field is the selection of non-bonded pa- rameters which are optimized to reproduce thermodynamic measurements in the con- densed phase. Specifically, the Martini model semi-quantitatively reproduces the free energy of hydration, the free energy of vaporization, and the partitioning free ener- gies between water and a collection of organic phases, obtained from the equilibrium densities in both phases: ∆Goil/aqueous _{= k}

BT ln (ρoil/ρaqueous). These calculations re-

quire long MD simulations of two-phase systems with very dilute concentrations of the target substance. Results agree to within 2kBT for many of these properties [212].

Systematic tuning to experimental partitioning free energies was used to select particle types for amino acids, represented with up to four beads which correspond to the polar character of the amino acid. Additionally, the pre-determined secondary structure modulates the character of the beads; backbone hydrogen bonds found in helices have reduced polar character [212]. While the building blocks for the Martini model were chosen to match thermodynamic data in general, any application of Martini model can be optimized by comparison to AA simulation, especially when designing bonded interactions to reproduce the protein structure.

In the Martini model, calculation of the partitioning free energy of water in hexade- cane agrees with the measurement of 25 kJ−mol−1 observed in Fischer titration [282]. More broadly, a combination of experiments and predictive modeling efforts have quantified partitioning free energies for other molecules [84, 352] and contributed to the parameter choices made by Marrink et al. [212]. Spin-echo nuclear magnetic resonance experiments provide self-diffusion data for water and alkanes [81, 169].

The hydration free energy can be calculated by comparing the partitioning of target molecules between liquid and vapor water phases, while the vaporization free energy can be calculated from the simulation of liquid-vapor equilibrium. In these simulations concentrations of 0.01 mole fraction provide a reasonable approximation of infinitely dilute solutions. A comparison of thermodynamic properties by Baron

et al. [25] showed that this CG model tends to overestimate the water-oil repulsion with free energies of vaporization and hydration which are systematically high, but still follow the correct trend.

The surface tension measures the free energy cost of adding area to the interface between solvents. Simulations were compared to drop volume tensiometry measure- ments with good agreement for water, vapor, and dodecane mixtures [8]. Electron density profiles from X-ray diffraction data on multilamellar arrays of bilayers provide a measure of the thickness. While neutron scattering is weaker, specific deuteration of different lipid components gives a local contrast agent without chemical modifica- tions [232].

It is clear that the coarse-grained models described in this review often share the same target data. In this section, we have summarized the most important experi- ments which inform the Martini model in order to demonstrate the breadth of the physics which these data capture. While the three CG models reviewed in this paper produce extremely rich physics, they draw on data sets with orders of magnitude greater detail and information. Some of the key differences between these models are summarized in table 2.1. For this reason, there is no one “correct” method for incor- porating these data into an accurate coarse-grained model. Indeed, it is impossible for any coarse-grained model to simultaneously match thermodynamic, structural, and kinetic features perfectly. Therefore, it is necessary for model developers to choose specific experimental results which are relevant to the desired application. In the next section we will take a deeper look at how these experiments can be used in a general coarse-grained model.