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Register a new userInfluence of Molecular Solvation on the Conformation of Star Polymers
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We have used neutron scattering to investigate the influence of concentration on the conformation of a star polymer. By varying the contrast between the solvent and isotopically labeled stars, we obtain the distributions of polymer and solvent within a star polymer from analysis of scattering data. A correlation between the local desolvation and the inward folding of star branches is discovered. From the perspective of thermodynamics, we find an analogy between the mechanism of polymer localization driven by solvent depletion and that of the hydrophobic collapse of polymers in solutions.
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The long-ranged nature of the Coulomb potential requires a proper accounting for the influence of even distant electrostatic boundaries in the determination of the solvation free energy of a charged solute. We introduce an exact rewriting of the free energy change upon charging a solute that explicitly isolates the contribution from these boundaries and quantifies the impact of the different boundaries on the free energy. We demonstrate the importance and advantages of appropriately referencing the electrostatic potential to that of the vacuum through the study of several simple model charge distributions, for which we can isolate an analytic contribution from the boundaries that can be readily evaluated in computer simulations of molecular systems. Finally, we highlight that the constant potential of the bulk dielectric phase - the Bethe potential - cannot contribute to the solvation thermodynamics of a single charged solute when the charge distributions of the solvent and solute do not overlap in relevant configurations. But when the charge distribution of a single solute can overlap with the intramolecular charge distribution of solvent molecules, as is the case in electron holography, for example, the Bethe potential is needed when comparing to experiment. Our work may also provide insight into the validity of extra thermodynamic assumptions traditionally made during the experimental determination of single ion solvation free energies.
We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density of states obtained in advanced replica-exchange Monte Carlo simulations is analyzed by employing the recently developed generalized microcanonical inflection-point analysis method, which enables the identification of diverse structural phases and the construction of a suitably parameterized hyperphase diagram. It reveals that icosahedral phases dominate for polymers with asymmetric and narrow bond potentials, whereas polymers with symmetric and more elastic bonds tend to form amorphous structures with non-icosahedral cores. We also observe a hierarchy in the freezing transition behavior associated with the formation of the surface layer after nucleation.
Continuum models to handle solvent and electrolyte effects in an effective way have a long tradition in quantum-chemistry simulations and are nowadays also being introduced in computational condensed-matter and materials simulations. A key ingredient of continuum models is the choice of the solute cavity, i.e. the definition of the sharp or smooth boundary between the regions of space occupied by the quantum-mechanical (QM) system and the continuum embedding environment. Although most of the solute-based approaches developed lead to models with comparable and high accuracy when applied to small organic molecules, they can introduce significant artifacts when complex systems are considered. As an example, condensed-matter simulations often deal with supports that present open structures. Similarly, unphysical pockets of continuum solvent may appear in systems featuring multiple molecular components. Here, we introduce a solvent-aware approach to eliminate the unphysical effects where regions of space smaller than the size of a single solvent molecule could still be filled with a continuum environment. We do this by defining a smoothly varying solute cavity that overcomes several of the limitations of straightforward solute-based definitions. This new approach applies to any smooth local definition of the continuum interface, being it based on the electronic density or the atomic positions of the QM system. It produces boundaries that are continuously differentiable with respect to the QM degrees of freedom, leading to accurate forces and/or Kohn-Sham potentials. Benchmarks on semiconductor substrates and on explicit water substrates confirm the flexibility and the accuracy of the approach and provide a general set of parameters for condensed-matter systems featuring open structures and/or explicit liquid components.
The solvation model proposed by Fattebert and Gygi [Journal of Computational Chemistry 23, 662 (2002)] and Scherlis et al. [Journal of Chemical Physics 124, 074103 (2006)] is reformulated, overcoming some of the numerical limitations encountered and extending its range of applicability. We first recast the problem in terms of induced polarization charges that act as a direct mapping of the self-consistent continuum dielectric; this allows to define a functional form for the dielectric that is well behaved both in the high-density region of the nuclear charges and in the low-density region where the electronic wavefunctions decay into the solvent. Second, we outline an iterative procedure to solve the Poisson equation for the quantum fragment embedded in the solvent that does not require multi-grid algorithms, is trivially parallel, and can be applied to any Bravais crystallographic system. Last, we capture some of the non-electrostatic or cavitation terms via a combined use of the quantum volume and quantum surface [Physical Review Letters 94, 145501 (2005)] of the solute. The resulting self-consistent continuum solvation (SCCS) model provides a very effective and compact fit of computational and experimental data, whereby the static dielectric constant of the solvent and one parameter allow to fit the electrostatic energy provided by the PCM model with a mean absolute error of 0.3 kcal/mol on a set of 240 neutral solutes. Two parameters allow to fit experimental solvation energies on the same set with a mean absolute error of 1.3 kcal/mol. A detailed analysis of these results, broken down along different classes of chemical compounds, shows that several classes of organic compounds display very high accuracy, with solvation energies in error of 0.3-0.4 kcal/mol, whereby larger discrepancies are mostly limited to self-dissociating species and strong hydrogen-bond forming compounds.
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 polymer collapse proceeds through the formation of a sufficiently large non-polar cluster, and that collective water density fluctuations play an important role in stabilizing such a cluster. We also study the collapse of the hydrophobic polymer in octane, a non-polar solvent, and interestingly, we find that the mechanistic details of the transition are qualitatively similar to that in water.
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