521 research outputs found
Revised self-consistent continuum solvation in electronic-structure calculations
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.Comment: The following article has been accepted by The Journal of Chemical
Physics. After it is published, it will be found at
http://link.aip.org/link/?jcp
Progetto di una Casa della Musica a Pisa. Architettura e Acustica
Progetto di un edificio ipogeo per la music
Transport properties of room temperature ionic liquids from classical molecular dynamics
Room Temperature Ionic Liquids (RTILs) have attracted much of the attention
of the scientific community in the past decade due the their novel and highly
customizable properties. Nonetheless their high viscosities pose serious
limitations to the use of RTILs in practical applications. To elucidate some of
the physical aspects behind transport properties of RTILs, extensive classical
molecular dynamics (MD) calculations are reported. Bulk viscosities and ionic
conductivities of butyl-methyl-imidazole based RTILs are presented over a wide
range of temperatures. The dependence of the properties of the liquids on
simulation parameters, e.g. system size effects and choice of the interaction
potential, is analyzed
Electrostatics of solvated systems in periodic boundary conditions
Continuum solvation methods can provide an accurate and inexpensive embedding
of quantum simulations in liquid or complex dielectric environments.
Notwithstanding a long history and manifold applications to isolated systems in
open boundary conditions, their extension to materials simulations ---
typically entailing periodic-boundary conditions --- is very recent, and
special care is needed to address correctly the electrostatic terms. We discuss
here how periodic-boundary corrections developed for systems in vacuum should
be modified to take into account solvent effects, using as a general framework
the self-consistent continuum solvation model developed within plane-wave
density-functional theory [O. Andreussi et al. J. Chem. Phys. 136, 064102
(2012)]. A comprehensive discussion of real-space and reciprocal-space
corrective approaches is presented, together with an assessment of their
ability to remove electrostatic interactions between periodic replicas.
Numerical results for zero-dimensional and two-dimensional charged systems
highlight the effectiveness of the different suggestions, and underline the
importance of a proper treatement of electrostatic interactions in
first-principles studies of charged systems in solution
Uncoupling System and Environment Simulation Cells for Fast-Scaling Modeling of Complex Continuum Embeddings
Continuum solvation models are becoming increasingly relevant in condensed
matter simulations, allowing to characterize materials interfaces in the
presence of wet electrified environments at a reduced computational cost with
respect to all atomistic simulations. However, some challenges with the
implementation of these models in plane-wave simulation packages still
persists, especially when the goal is to simulate complex and heterogeneous
environments. Among these challenges is the computational cost associated with
large heterogeneous environments, which in plane-wave simulations has a direct
effect on the basis-set size and, as a result, on the cost of the electronic
structure calculation. Moreover, the use of periodic simulation cells are not
well-suited for modeling systems embedded in semi-infinite media, which is
often the case in continuum solvation models. To address these challenges, we
present the implementation of a double-cell formalism, in which the simulation
cell used for the continuum environment is uncoupled from the one used for the
electronic-structure simulation of the quantum-mechanical system. This allows
for a larger simulation cell to be used for the environment, without
significantly increasing computational time. In this work, we show how the
double-cell formalism can be used as an effective PBC correction scheme for
non-periodic and partially periodic systems. The accuracy of the double-cell
formalism is tested using representative examples with different
dimensionalities, both in vacuum and in a continuum dielectric environment.
Fast convergence and good speedups are observed for all the simulation setups,
provided the quantum-mechanical simulation cell is chosen to completely fit the
electronic density of the system
A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments
The computational study of chemical reactions in complex, wet environments is
critical for applications in many fields. It is often essential to study
chemical reactions in the presence of applied electrochemical potentials,
taking into account the non-trivial electrostatic screening coming from the
solvent and the electrolytes. As a consequence the electrostatic potential has
to be found by solving the generalized Poisson and the Poisson-Boltzmann
equation for neutral and ionic solutions, respectively. In the present work
solvers for both problems have been developed. A preconditioned conjugate
gradient method has been implemented to the generalized Poisson equation and
the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the
minimization problem with some ten iterations of a ordinary Poisson equation
solver. In addition, a self-consistent procedure enables us to solve the
non-linear Poisson-Boltzmann problem. Both solvers exhibit very high accuracy
and parallel efficiency, and allow for the treatment of different boundary
conditions, as for example surface systems. The solver has been integrated into
the BigDFT and Quantum-ESPRESSO electronic-structure packages and will be
released as an independent program, suitable for integration in other codes
Water on Pt(111): the importance of proton disorder
The structure of a water adlayer on Pt(111) surface is investigated by
extensive first principle calculations. Only allowing for proton disorder the
ground state energy can be found. This results from an interplay between
water/metal chemical bonding and the hydrogen bonding of the water network. The
resulting short O-Pt distance accounts for experimental evidences. The novelty
of these results shed a new light on relevant aspects of water-metal
interaction.Comment: 10 pages 4 figures (color
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