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Register a new userCoupling hydrophobic, dispersion, and electrostatic contributions in continuum solvent models
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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.
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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.
Continuum solvation models enable efficient first principles calculations of chemical reactions in solution, but require extensive parametrization and fitting for each solvent and class of solute systems. Here, we examine the assumptions of continuum solvation models in detail and replace empirical terms with physical models in order to construct a minimally-empirical solvation model. Specifically, we derive solvent radii from the nonlocal dielectric response of the solvent from ab initio calculations, construct a closed-form and parameter-free weighted-density approximation for the free energy of the cavity formation, and employ a pair-potential approximation for the dispersion energy. We show that the resulting model with a single solvent-independent parameter: the electron density threshold ($n_c$), and a single solvent-dependent parameter: the dispersion scale factor ($s_6$), reproduces solvation energies of organic molecules in water, chloroform and carbon tetrachloride with RMS errors of 1.1, 0.6 and 0.5 kcal/mol respectively. We additionally show that fitting the solvent-dependent $s_6$ parameter to the solvation energy of a single non-polar molecule does not substantially increase these errors. Parametrization of this model for other solvents, therefore, requires minimal effort and is possible without extensive databases of experimental solvation free energies.
Janus -- or two-sided, asymmetrical -- charged membranes offer promise as ionic current rectifiers. In such systems, pores consisting of two regions of opposite charge can be used to generate a current from a gradient in salinity. The efficiency of Janus pores increases dramatically as their diameter becomes smaller. However, little is known about the underlying transport processes, both for water and ions, in Janus nanopores. In this work, the molecular basis for rectification in Janus nanopores is examined both at rest and in the presence of an applied electric field. By relying on detailed equilibrium and far-from-equilibrium simulations, using explicit models of water and ions, we analyse the structure and dynamics of all molecular species in solution, as well as the overall response of these asymmetric nanopore devices subject to a positive or negative bias, respectively. While there is no precedent for atomistic simulations of a functioning Janus pore, the calculations are able to reproduce key macroscopic experimental observations of asymmetric membranes, serving to establish the validity of the models adopted here. As opposed to the most popularly implemented continuum approaches, here a detailed view is presented of the molecular structures and characteristics that give rise to ionic rectification in such systems, including the local re-orientation of water in the pores and the segregation of ionic species. New insights for the technological development of practical nanofluidic devices are also presented on the basis of these findings.
Solvent can occupy up to ~70% of macromolecular crystals and hence having models that predict solvent distributions in periodic systems could improve in the interpretation of crystallographic data. Yet there are few implicit solvent models applicable to periodic solutes while crystallographic structures are commonly solved assuming a flat solvent model. Here we present a newly-developed periodic version of the 3D-RISM integral equation method that is able to solve for efficiently and describe accurately water and ions distributions in periodic systems; the code can compute accurate gradients that can be used in minimizations or molecular dynamics simulations. The new method includes an extension of the OZ equation needed to yield charge neutrality for charged solutes which requires an additional contribution to the excess chemical potential that has not been previously identified; this is an important consideration for nucleic acids or any other charged system where most or all of the counter- and co-ions are part of the disordered solvent. We present of several calculations of protein, RNA and small molecule crystals to show that X-ray scattering intensities and solvent structure predicted by the periodic 3D-RISM solvent model are in closer agreement with experiment than are intensities computed using the default flat solvent model in the refmac5 or phenix refinement programs, with the greatest improvement in the 2 to 4 {AA} range. Prospects for incorporating integral equation models into crystallographic refinement are discussed.
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