No Arabic abstract
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.
Recent studies on the solvation of atomistic and nanoscale solutes indicate that a strong coupling exists between the hydrophobic, dispersion, and electrostatic contributions to the solvation free energy, a facet not considered in current implicit solvent models. We suggest a theoretical formalism which accounts for coupling by minimizing the Gibbs free energy of the solvent with respect to a solvent volume exclusion function. The resulting differential equation is similar to the Laplace-Young equation for the geometrical description of capillary interfaces, but is extended to microscopic scales by explicitly considering curvature corrections as well as dispersion and electrostatic contributions. Unlike existing implicit solvent approaches, the solvent accessible surface is an output of our model. The presented formalism is illustrated on spherically or cylindrically symmetrical systems of neutral or charged solutes on different length scales. The results are in agreement with computer simulations and, most importantly, demonstrate that our method captures the strong sensitivity of solvent expulsion and dewetting to the particular form of the solvent-solute interactions.
Recent studies of the hydration of micro- and nanoscale solutes have demonstrated a strong {it coupling} between hydrophobic, dispersion and electrostatic contributions, a fact not accounted for in current implicit solvent models. We present a theoretical formalism which accounts for coupling by minimizing the Gibbs free energy with respect to a solvent volume exclusion function. The solvent accessible surface is output of our theory. Our method is illustrated with the hydration of alkane-assembled solutes on different length scales, and captures the strong sensitivity to the particular form of the solute-solvent interactions in agreement with recent computer simulations.
In this work, a systematic protocol is proposed to automatically parametrize implicit solvent models with polar and nonpolar components. The proposed protocol utilizes the classical Poisson model or the Kohn-Sham density functional theory (KSDFT) based polarizable Poisson model for modeling polar solvation free energies. For the nonpolar component, either the standard model of surface area, molecular volume, and van der Waals interactions, or a model with atomic surface areas and molecular volume is employed. Based on the assumption that similar molecules have similar parametrizations, we develop scoring and ranking algorithms to classify solute molecules. Four sets of radius parameters are combined with four sets of charge force fields to arrive at a total of 16 different parametrizations for the Poisson model. A large database with 668 experimental data is utilized to validate the proposed protocol. The lowest leave-one-out root mean square (RMS) error for the database is 1.33k cal/mol. Additionally, five subsets of the database, i.e., SAMPL0-SAMPL4, are employed to further demonstrate that the proposed protocol offers some of the best solvation predictions. The optimal RMS errors are 0.93, 2.82, 1.90, 0.78, and 1.03 kcal/mol, respectively for SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 test sets. These results are some of the best, to our best knowledge.
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.