1,013 research outputs found
Water at an electrochemical interface - a simulation study
The results of molecular dynamics simulations of the properties of water in
an aqueous ionic solution close to an interface with a model metallic electrode
are described. In the simulations the electrode behaves as an ideally
polarizable hydrophilic metal, supporting image charge interactions with
charged species, and it is maintained at a constant electrical potential with
respect to the solution so that the model is a textbook representation of an
electrochemical interface through which no current is passing. We show how
water is strongly attracted to and ordered at the electrode surface. This
ordering is different to the structure that might be imagined from continuum
models of electrode interfaces. Further, this ordering significantly affects
the probability of ions reaching the surface. We describe the concomitant
motion and configurations of the water and ions as functions of the electrode
potential, and we analyze the length scales over which ionic atmospheres
fluctuate. The statistics of these fluctuations depend upon surface structure
and ionic strength. The fluctuations are large, sufficiently so that the mean
ionic atmosphere is a poor descriptor of the aqueous environment near a metal
surface. The importance of this finding for a description of electrochemical
reactions is examined by calculating, directly from the simulation, Marcus free
energy profiles for transfer of charge between the electrode and a redox
species in the solution and comparing the results with the predictions of
continuum theories. Significant departures from the electrochemical textbook
descriptions of the phenomenon are found and their physical origins are
characterized from the atomistic perspective of the simulations.Comment: 29 pages, 15 figure
Fully Polarizable QM/Fluctuating Charge Approach to Two-Photon Absorption of Aqueous Solutions
We present the extension of the quantum/classical polarizable fluctuating
charge model to the calculation of single residues of quadratic response
functions, as required for the computational modeling of two-photon absorption
cross-sections. By virtue of a variational formulation of the quantum/classical
polarizable coupling, we are able to exploit an atomic orbital-based
quasienergy formalism to derive the additional coupling terms in the response
equations. Our formalism can be extended to the calculation of arbitrary order
response functions and their residues. The approach has been applied to the
challenging problem of one- and two-photon spectra of rhodamine 6G (R6G) in
aqueous solution. Solvent effects on one- and two-photon spectra of R6G in
aqueous solution have been analyzed by considering three different approaches,
from a continuum (QM/PCM) to two QM/MM models (non-polarizable QM/TIP3P and
polarizable QM/FQ). Both QM/TIP3P and QM/FQ simulated OPA and TPA spectra show
that the inclusion of discrete water solvent molecules is essential to increase
the agreement between theory and experiment. QM/FQ has been shown to give the
best agreement with experiments
The Polarizable Continuum Model Goes Viral! Extensible, Modular and Sustainable Development of Quantum Mechanical Continuum Solvation Models
Synergistic theoretical and experimental approaches to challenging chemical problems have become more and more widespread, due to the availability of efficient and accurate ab initio quantum chemical models. Limitations to such an approach do, however, still exist. The vast majority of chemical phenomena happens in complex environments, where the molecule of interest can interact with a large number of other moieties, solvent molecules or residues in a protein. These systems represent an ongoing challenge to our modelling capabilities, especially when high accuracy is required for the prediction of exotic and novel molecular properties. How to achieve the insight needed to understand and predict the physics and chemistry of such complex systems is still an open question. I will present our efforts in answering this question based on the development of the polarizable continuum model for solvation. While the solute is described by a quantum mechanical method, the surrounding environment is replaced by a structureless continuum dielectric. The mutual polarization of the solute-environment system is described by classical electrostatics. Despite its inherent simplifications, the model contains the basic mathematical features of more refined explicit quantum/classical polarizable models. Leveraging this fundamental similarity, we show how the inclusion of environment effects for relativistic and nonrelativistic quantum mechanical Hamiltonians, arbitrary order response properties and high-level electron correlation methods can be transparently derived and implemented. The computer implementation of the polarizable continuum model is central to the work presented in this dissertation. The quantum chemistry software ecosystem suffers from a growing complexity. Modular programming offers an extensible, flexible and sustainable paradigm to implement new features with reduced effort. PCMSolver, our open-source application programming interface, can provide continuum solvation functionality to any quantum chemistry software: continuum solvation goes viral. Our strategy affords simpler programming workflows, more thorough testing and lower overall code complexity. As examples of the flexibility of our implementation approach, we present results for the continuum modelling of non homogeneous environments and how wavelet-based numerical methods greatly outperform the accuracy of traditional methods usually employed in continuum solvation models
Electronic structure of small surfactants: a continuum solvation study
Source: DOI:
10.1021/acs.jpcc.6b05309The e ect of surfaces and interfaces on the structure and properties of molecules is of
a great interest in a number of biological and technological applications. Nevertheless,
such an investigation is extremely challenging from an experimental point of view,
due to the bidimensionality of the environment. In recent years, we have developed
a framework to study molecules at surfaces and interfaces, by means of a continuum
approach. In the present study, we extend our model by showing the e ect of interfacial
solvation on molecular properties and by re ning the description of the transfer process,
making use of a proper Boltzmann averaging of the orientational degrees of freedom.
Our ndings are in substantial agreement with previous simulations, for the energetics
of the transfer process, but yield a somehow di erent description of the molecular
electronic structure. Both the agreement on the energetics and the disagreement on
the properties are motivated in light of the role played by non-electrostatic e ects in
the solvation process
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
Understanding the Effect of Cation and Solvation on the Structure and Reactivity of Nitrile Anions
This Ph.D. dissertation is focused on the investigation the structure of nitrile anion containing molecules and how the structure and reactivity of those molecules are affected by solvation and counter ion. A systematic approach was employed in this investigation, beginning with an evaluation of the accuracy of three commonly used model chemistries (Hartree-Fock (HF), Second-order Møller-Plesset perturbation theory (MP2), the Becke three-parameter exchange functional coupled with the nonlocal correlation functional of Lee, Yang, and Parr (B3LYP), all paired with the 6-31+G(d) basis set). A series of complexes of various cations with a number of explicit molecules of tetrahydrofuran (THF) and dimethyl ether (DME) were studied with these model chemistries and the results were compared, where possible, with experimental results. From this work, it was determined that the B3LYP models gave the most accurate results for the complexes in question. This work was then extended to acetonitrile anion containing complexes of solvent and cation. Based on the results of that extension, it was determined that cation size and charge density on the cation were critical factors in determining the structure of the acetonitrile anion molecule and in determining if the anion was metalated at the nitrogen or α-carbon position, with larger cations favoring carbon metalation and more significant deformation of the α-carbon from the expected sp2 hybridization. The final aspect of this dissertation was the determination of reaction coordinate energy profiles for a pair of substitution reactions involving nitrile anion containing cycloaliphatic molecules. The results of this study showed that, due to steric and kinetic factors, the axial products and transitions states associated with these reactions were favored, and that the degree of preference was kinetically controlled
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