1,947 research outputs found
Variational Methods for Biomolecular Modeling
Structure, function and dynamics of many biomolecular systems can be
characterized by the energetic variational principle and the corresponding
systems of partial differential equations (PDEs). This principle allows us to
focus on the identification of essential energetic components, the optimal
parametrization of energies, and the efficient computational implementation of
energy variation or minimization. Given the fact that complex biomolecular
systems are structurally non-uniform and their interactions occur through
contact interfaces, their free energies are associated with various interfaces
as well, such as solute-solvent interface, molecular binding interface, lipid
domain interface, and membrane surfaces. This fact motivates the inclusion of
interface geometry, particular its curvatures, to the parametrization of free
energies. Applications of such interface geometry based energetic variational
principles are illustrated through three concrete topics: the multiscale
modeling of biomolecular electrostatics and solvation that includes the
curvature energy of the molecular surface, the formation of microdomains on
lipid membrane due to the geometric and molecular mechanics at the lipid
interface, and the mean curvature driven protein localization on membrane
surfaces. By further implicitly representing the interface using a phase field
function over the entire domain, one can simulate the dynamics of the interface
and the corresponding energy variation by evolving the phase field function,
achieving significant reduction of the number of degrees of freedom and
computational complexity. Strategies for improving the efficiency of
computational implementations and for extending applications to coarse-graining
or multiscale molecular simulations are outlined.Comment: 36 page
Electroneutrality Breakdown and Specific Ion Effects in Nanoconfined Aqueous Electrolytes Observed by NMR
Ion distribution in aqueous electrolytes near the interface plays critical
roles in electrochemical, biological and colloidal systems and is expected to
be particularly significant inside nanoconfined regions. Electroneutrality of
the total charge inside nanoconfined regions is commonly assumed a priori in
solving ion distribution of aqueous electrolytes nanoconfined by uncharged
hydrophobic surfaces with no direct experimental validation. Here, we use a
quantitative nuclear magnetic resonance approach to investigate the properties
of aqueous electrolytes nanoconfined in graphitic-like nanoporous carbon.
Substantial electroneutrality breakdown in nanoconfined regions and very
asymmetric responses of cations and anions to the charging of nanoconfining
surfaces are observed. The electroneutrality breakdown is shown to depend
strongly on the propensity of anions toward the water-carbon interface and such
ion-specific response follows generally the anion ranking of the Hofmeister
series. The experimental observations are further supported by numerical
evaluation using the generalized Poisson-Boltzmann equationComment: 26 pages, 3 figure
Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions
Determining the solvation free energies of single ions in water is one of the
most fundamental problems in physical chemistry and yet many unresolved
questions remain. In particular, the ability to decompose the solvation free
energy into simple and intuitive contributions will have important implications
for models of electrolyte solution. Here, we provide definitions of the various
types of single ion solvation free energies based on different simulation
protocols. We calculate solvation free energies of charged hard spheres using
density functional theory interaction potentials with molecular dynamics
simulation (DFT-MD) and isolate the effects of charge and cavitation, comparing
to the Born (linear response) model. We show that using uncorrected Ewald
summation leads to unphysical values for the single ion solvation free energy
and that charging free energies for cations are approximately linear as a
function of charge but that there is a small non-linearity for small anions.
The charge hydration asymmetry (CHA) for hard spheres, determined with quantum
mechanics, is much larger than for the analogous real ions. This suggests that
real ions, particularly anions, are significantly more complex than simple
charged hard spheres, a commonly employed representation.Comment: 28 pages, 5 figure
The Poisson-Boltzmann model for implicit solvation of electrolyte solutions: Quantum chemical implementation and assessment via Sechenov coefficients.
We present the theory and implementation of a Poisson-Boltzmann implicit solvation model for electrolyte solutions. This model can be combined with arbitrary electronic structure methods that provide an accurate charge density of the solute. A hierarchy of approximations for this model includes a linear approximation for weak electrostatic potentials, finite size of the mobile electrolyte ions, and a Stern-layer correction. Recasting the Poisson-Boltzmann equations into Euler-Lagrange equations then significantly simplifies the derivation of the free energy of solvation for these approximate models. The parameters of the model are either fit directly to experimental observables-e.g., the finite ion size-or optimized for agreement with experimental results. Experimental data for this optimization are available in the form of Sechenov coefficients that describe the linear dependence of the salting-out effect of solutes with respect to the electrolyte concentration. In the final part, we rationalize the qualitative disagreement of the finite ion size modification to the Poisson-Boltzmann model with experimental observations by taking into account the electrolyte concentration dependence of the Stern layer. A route toward a revised model that captures the experimental observations while including the finite ion size effects is then outlined. This implementation paves the way for the study of electrochemical and electrocatalytic processes of molecules and cluster models with accurate electronic structure methods
Interplay of local hydrogen-bonding and long-ranged dipolar forces in simulations of confined water
Spherical truncations of Coulomb interactions in standard models for water
permit efficient molecular simulations and can give remarkably accurate results
for the structure of the uniform liquid. However truncations are known to
produce significant errors in nonuniform systems, particularly for
electrostatic properties. Local molecular field (LMF) theory corrects such
truncations by use of an effective or restructured electrostatic potential that
accounts for effects of the remaining long-ranged interactions through a
density-weighted mean field average and satisfies a modified Poisson's equation
defined with a Gaussian-smoothed charge density. We apply LMF theory to three
simple molecular systems that exhibit different aspects of the failure of a
naive application of spherical truncations -- water confined between
hydrophobic walls, water confined between atomically-corrugated hydrophilic
walls, and water confined between hydrophobic walls with an applied electric
field. Spherical truncations of 1/r fail spectacularly for the final system in
particular, and LMF theory corrects the failings for all three. Further, LMF
theory provides a more intuitive way to understand the balance between local
hydrogen bonding and longer-ranged electrostatics in molecular simulations
involving water.Comment: Submitted to PNA
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