Characterizing the Interplay between Polymer Solvation and Conformation

Abstract

Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between solvation and conformation. Using specialized molecular simulations, here we perform such a characterization for a hydrophobic polymer solvated in water. We find that an external potential, which unfavorably perturbs the polymer hydration waters, can trigger a coil-to-globule or collapse transition, and that the relative stabilities of the collapsed and extended states can be quantified by the strength of the requisite potential. Our results also provide mechanistic insights into the collapse transition, highlighting that the bottleneck to polymer collapse is the formation of a sufficiently large cluster, and the collective dewetting of such a cluster. We also study the collapse of the hydrophobic polymer in octane, a nonpolar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.

Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multimolecular and Solvent-Inclusive Collective Variables

“…A trivial strategy to treat the permutational invariance of a solvent bath is to simply ignore the solvent coordinates and assume that the solvent effects are sufficiently strongly imprinted on the solute conformational dynamics that they can be driven implicitly by biasing solute-centric CVs . Patel, Varilly, Chandler, and Garde developed the indirect umbrella sampling (INDUS) approach to drive water density fluctuations in user-defined control volumes and have used this technique to drive the sampling of wetting/dewetting transitions. , Zou et al employed CVs based on coordination numbers, Steinhardt bond order parameters, interfacial water density, intermolecular angles, and pair orientational entropy and combined these within the SPIB framework to drive the sampling of crystal nucleation and polymorph formation . Rizzi et al combined CVs describing the solvent coordination number and solvent structure around a binding pocket with the deep linear discriminant analysis (Deep-LDA) approach to incorporate water coordinates in driving the sampling of host–guest interactions …”

Potential Energy Surfaces Sampled in Cremer–Pople Coordinates and Represented by Common Force Field Functionals for Small Cyclic Molecules

“…Non-aromatic cyclic molecules exhibit complex potential energy surfaces (PESs) with multiple geometrically distinct conformers − connected via multiple energy paths. The complexity of the PESs affects their thermodynamic properties − and biological activities. − Because of their importance as building blocks of biological and chemical compounds, − cyclic moieties have long been studied experimentally ,,− and theoretically. ,,− Thorough characterization and representation of the cyclic PESs are important for understanding and predicting the structure–property relationships of many molecules.…”

Potential-Energy Surfaces Sampled in Cremer–Pople Coordinates and Represented by Common Force Field Functionals for Small-cyclic Molecules

“…Non-aromatic cyclic molecules exhibit complex potential energy surfaces (PESs) with multiple geometrically distinct conformers [1][2][3][4] connected via multiple energy paths. The complexity of the PESs affects their thermodynamic properties [5][6][7][8][9][10][11][12] and biological activities [12][13][14][15] . Because of their importance as building blocks of biological and chemical compounds [16][17][18][19][20][21][22] , cyclic moieties have long been studied experimentally 12,18,[23][24][25][26][27] and theoretically 12,26,[28][29][30] .…”