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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 is 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 periodic boundary conditions correction scheme for nonperiodic 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 homogeneous 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. [ABSTRACT FROM AUTHOR]

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 equations 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 for the solution of the generalized Poisson equation and the linear regime of the Poisson-Boltzmann, allowing to solve iteratively the minimization problem with some ten iterations of the 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 periodic, free, and slab boundary conditions. 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. [ABSTRACT FROM AUTHOR]

The recently developed self-consistent continuum solvation model (SCCS) [O. Andreussi, I. Dabo, and N. Marzari, J. Chem. Phys. 136, 064102 (2012)] is applied here to charged species in aqueous solutions. Describing ions in solution represents a great challenge because of the large electrostatic interactions between the solute and the solvent. The SCCS model is tested over 106 monocharged species, both cations and anions, and we demonstrate its flexibility, notwithstanding its much reduced set of parameters, to describe charged species in solution. Remarkably low mean absolute errors are obtained with values of 2.27 and 5.54 kcal/mol for cations and anions, respectively. These results are comparable or better than the state of the art to describe solvation of charged species in water. Finally, differences of behavior between cations and anions are discussed. [ABSTRACT FROM AUTHOR]

Solvation effects profoundly influence the characteristics and behavior of chemical systems in liquid solutions. The interaction between solute and solvent molecules intricately impacts solubility, reactivity, stability, and various chemical processes. Continuum solvation models gained prominence in quantum chemistry by implicitly capturing these interactions and enabling efficient investigations of diverse chemical systems in solution. In comparison, continuum solvation models in condensed matter simulation are very recent. Among these, the self-consistent continuum solvation (SCCS) and the soft-sphere continuum solvation models (SSCS) have been among the first to be successfully parameterized and extended to model periodic systems in aqueous solutions and electrolytes. As most continuum approaches, these models depend on a number of parameters that are linked to experimental or theoretical properties of the solvent, or that can be tuned based on reference data. Here, we present a systematic parameterization of the SSCS model for over 100 nonaqueous solvents. We validate the model's efficacy across diverse solvent environments by leveraging experimental solvation-free energies and partition coefficients from comprehensive databases. The average root means square error over all the solvents was calculated as 0.85 kcal/mol which is below the chemical accuracy (1 kcal/mol). Similarly to what has been reported by Hille et al. (J. Chem. Phys. 2019, 150, 041710.) for the SCCS model, a single-parameter model accurately reproduces experimental solvation energies, showcasing the transferability and predictive power of these continuum approaches. Our findings underscore the potential for a unified approach to predict solvation properties, paving the way for enhanced computational studies across various chemical environments., (© 2023 Wiley Periodicals LLC.)

The computational modeling of electrochemical interfaces and their applications in electrocatalysis has attracted great attention in recent years. While tremendous progress has been made in this area, however, the accurate atomistic descriptions at the electrode/electrolyte interfaces remain a great challenge. The Computational Hydrogen Electrode (CHE) method and continuum modeling of the solvent and electrolyte interactions form the basis for most of these methodological developments. Several posterior corrections have been added to the CHE method to improve its accuracy and widen its applications. The most recently developed grand canonical potential approaches with the embedded diffuse layer models have shown considerable improvement in defining interfacial interactions at electrode/electrolyte interfaces over the state-of-the-art computational models for electrocatalysis. In this Review, we present an overview of these different computational models developed over the years to quantitatively probe the thermodynamics and kinetics of electrochemical reactions in the presence of an electrified catalyst surface under various electrochemical environments. We begin our discussion by giving a brief picture of the different continuum solvation approaches, implemented within the ab initio method to effectively model the solvent and electrolyte interactions. Next, we present the thermodynamic and kinetic modeling approaches to determine the activity and stability of the electrocatalysts. A few applications to these approaches are also discussed. We conclude by giving an outlook on the different machine learning models that have been integrated with the thermodynamic approaches to improve their efficiency and widen their applicability., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Motivated by the need to find good electrocatalysts for water oxidation and O 2 reduction, composed of nontoxic and earth-abundant elements, a systematic screening of two-dimensional (2D) transition metal dichalcogenides (TMDCs) is performed. To identify compounds that are intrinsically active and can fully take advantage of the high surface area of 2D catalysts, this study focuses on the properties of the ideal basal planes of 2D TMDCs, in the 2H, 1T, and 1T' phases. Over two hundred materials proposed in computational databases are studied by means of first-principles-based simulations coupled with continuum embedding models to account for the presence of electrochemical environments. The best candidates with overpotentials for the oxygen evolution and reduction reactions (OER and ORR) lower than 0.5 V under acidic conditions and higher stability against degradation in electrochemical environments are selected. For OER, the designed workflow identifies one active and thermodynamically stable material, and seven materials that are metastable at the oxidative potentials and acidic pH. On the other hand, for ORR, we identify 20 materials with overpotentials less than 0.5 V. Among these compounds, six bifunctional materials have been experimentally reported, with 1T-NbTe 2 and 1T'-MoTe 2 being the best performing catalysts for OER and ORR, respectively.

Some organic pollutants in snowpacks undergo faster photodegradation than in solution. One possible explanation for such effect is that their UV-visible absorption spectra are shifted toward lower energy when the molecules are adsorbed at the air-ice interface. However, such bathochromic shift is difficult to measure experimentally. Here, we employ a multiscale/multimodel approach that combines classical and first-principles molecular dynamics, quantum chemical methods, and statistical learning to compute the light absorption spectra of two phenolic molecules in different solvation environments at the relevant thermodynamic conditions. Our calculations provide an accurate estimate of the bathochromic shift of the lowest-energy UV-visible absorption band when these molecules are adsorbed at the air-ice interface, and they shed light into its molecular origin.

Snowpacks contain a wide variety of inorganic and organic compounds, including some that absorb sunlight and undergo direct photoreactions. How the rates of these reactions in, and on, ice compare to rates in water is unclear: some studies report similar rates, while others find faster rates in/on ice. Further complicating our understanding, there is conflicting evidence whether chemicals react more quickly at the air-ice interface compared to in liquid-like regions (LLRs) within the ice. To address these questions, we measured the photodegradation rate of guaiacol (2-methoxyphenol) in various sample types, including in solution, in ice, and at the air-ice interface of nature-identical snow. Compared to aqueous solution, we find modest rate constant enhancements (increases of 3- to 6-fold) in ice LLRs, and much larger enhancements (of 17- to 77-fold) at the air-ice interface of nature-identical snow. Our computational modeling suggests the absorption spectrum for guaiacol red-shifts and increases on ice surfaces, leading to more light absorption, but these changes explain only a small portion (roughly 2 to 9%) of the observed rate constant enhancements in/on ice. This indicates that increases in the quantum yield are primarily responsible for the increased photoreactivity of guaiacol on ice; relative to solution, our results suggest that the quantum yield is larger by a factor of roughly 3-6 in liquid-like regions and 12-40 at the air-ice interface.

Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented using localized basis sets of reduced size, leaving no variational flexibility for the extra electron to delocalize. Alternatively, a recent approach exploiting DFT evaluations of total energies on electronic densities optimized at the Hartree-Fock (HF) level has been reported, showing that the self-interaction-free HF densities are able to lead to an improved description of the additional electron, returning affinities in close agreement with the experiments. Nonetheless, such an approach can fail when the HF densities are too inaccurate. Here, an alternative approach is presented, in which an embedding environment is used to stabilize the anion in a bound configuration. Similar to the HF case, when computing total energies at the DFT level on these corrected densities, electron affinities in very good agreement with experiments can be recovered. The effect of the environment can be evaluated and removed by an extrapolation of the results to the limit of vanishing embedding. Apart from the definition of the domain of the embedding potential, the approach is free from parameters and it can be easily applied to DFT calculations with delocalized basis sets, e.g., plane waves, for which alternative approaches are either not viable or more computationally demanding. The proposed extrapolation strategy can be thus applied also to extended systems, as often studied in condensed-matter physics and materials science, and we illustrate how the embedding environment can be exploited to determine the energy of an adsorbing anion, here a chloride ion on a metal surface, whose charge configuration would be incorrectly predicted by standard density functionals.

Continuum models of solvation are widespread tools for the prediction of solvation free energies of small molecular compounds from first principles. However, the continuum approximation at the core of these approaches limits their accuracy for the modeling of the aqueous solvation of compounds with highly polarized residue or of charged species. This is due to the fact that straightforward definitions of the continuum interface do not account for the reorganization effects induced by these solutes on the positions of surrounding solvent molecules. This kind of problem is usually overcome by stretching the definition of the continuum model, i.e., by using chemical intuition to adjust (usually shrinking) the size of the solvation interface close to the polarized/charged atoms. Nonetheless, this strategy introduces a significant number of additional parameters that need to be tuned and, at the same time, deters the model's transferability. A transferable solution is instead represented by an improved definition of the continuum interface, able to automatically account for the polarization/charge state of the embedded system. Following recent approaches in the literature, the component of the solute's electric field normal to the interface can be used as an effective proxy for the net charge of the embedded system. Here we show a simple definition of this field-aware approach as applied to the recently proposed soft-sphere continuum solvation (SSCS) method. In this model, each soft sphere composing the interface is allowed to readjust as a function of the value of the field flux through its surface. This effect introduces a complex dependence of the interface function on both the electronic and the ionic degrees of freedom of the solute. To account for this dependence during optimization procedures (e.g., the SCF loop and geometry optimization algorithms), the analytic derivatives of the new interface are reported and validated with their numerical counterparts. Application of the field-aware procedure to molecular compounds showing pathological behaviors with the standard SSCS approach show that significant improvements can be achieved by specifically tuning the newly introduced parameters.

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. The cavity, which should really reflect the region of space accessible to the degrees of freedom of the environmental components (the solvent), is usually defined by an exclusion approach in terms of the degrees of freedom of the system (the solute), typically, the atomic position of the QM system or its electronic density. 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, i.e., low-density materials that have regions of space in which a continuum environment could penetrate, while a real solvent would not be able to. Similarly, unphysical pockets of continuum solvent may appear in systems featuring multiple molecular components, e.g., when dealing with hybrid QM/continuum approaches to solvation that involve introducing explicit solvent molecules around the solvated system. 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, it being 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. The additional parameters involved in the solvent-aware interfaces can be set according to geometrical principles or can be converged to improve accuracy in complex multicomponent systems. 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 electrolyte models represent a practical tool to account for the presence of the diffuse layer at electrochemical interfaces. However, despite the increasing popularity of these in the field of materials science, it remains unclear which features are necessary in order to accurately describe interface-related observables such as the differential capacitance (DC) of metal electrode surfaces. We present here a critical comparison of continuum diffuse-layer models that can be coupled to an atomistic first-principles description of the charged metal surface in order to account for the electrolyte screening at electrified interfaces. By comparing computed DC values for the prototypical Ag(100) surface in an aqueous solution to experimental data, we validate the accuracy of the models considered. Results suggest that a size-modified Poisson-Boltzmann description of the electrolyte solution is sufficient to qualitatively reproduce the main experimental trends. Our findings also highlight the large effect that the dielectric cavity parameterization has on the computed DC values.

We discuss grand canonical simulations based on density-functional theory to study the thermodynamic properties of electrochemical interfaces of metallic electrodes in aqueous environments. Water is represented using implicit solvation, here via the self-consistent continuum solvation (SCCS) model, providing a charge-density dependent dielectric boundary. The electrochemical double layer is accounted for in terms of a phenomenological continuum description. It is shown that the experimental potentials of zero charge and interfacial capacitances can be reproduced for an optimized SCCS parameter set [ρ min = 0.0013, ρ max = 0.010 25]. By performing a detailed derivation and analysis of the interface energetics for selected electrochemical systems, we are able to relate the widely used approach of the computational hydrogen electrode (CHE) to a general grand canonical description of electrified interfaces. In particular, charge-neutral CHE results are shown to be an upper-boundary estimate for the grand canonical interfacial free energies. In order to demonstrate the differences between the CHE and full grand canonical calculations, we study the pristine (100), (110), and (111) surfaces for Pt, Au, Cu, and Ag, and H or Cl electrosorbed on Pt. The calculations support the known surface reconstructions in the aqueous solution for Pt and Au. Furthermore, the predicted potential-pH dependence of proton coverage, surface charge, and interfacial pseudocapacitance for Pt is found to be in close agreement with experimental or other theoretical data as well as the predicted equilibrium shapes for Pt nanoparticles. Finally, Cl is found to interact more strongly than H with the interfacial fields, leading to significantly altered interface energetics and structure upon explicit application of an electrode potential. This work underscores the strengths and eventual limits of the CHE approach and might guide further understanding of the thermodynamics of electrified interfaces.

In catalysis science stability is as crucial as activity and selectivity. Understanding the degradation pathways occurring during operation and developing mitigation strategies will eventually improve catalyst design, thus facilitating the translation of basic science to technological applications. Herein, we reveal the unique and general degradation mechanism of metallic nanocatalysts during electrochemical CO 2 reduction, exemplified by different sized copper nanocubes. We follow their morphological evolution during operation and correlate it with the electrocatalytic performance. In contrast with the most common coalescence and dissolution/precipitation mechanisms, we find a potential-driven nanoclustering to be the predominant degradation pathway. Grand-potential density functional theory calculations confirm the role of the negative potential applied to reduce CO 2 as the main driving force for the clustering. This study offers a novel outlook on future investigations of stability and degradation reaction mechanisms of nanocatalysts in electrochemical CO 2 reduction and, more generally, in electroreduction reactions.

Classical molecular dynamics is more and more often coupled to quantum mechanical based techniques as a statistical tool to sample configurations of molecular systems embedded in complex environments. Nonetheless, the classical potentials describing the molecular systems are seldom parametrized to reproduce electronic processes, such as electronic excitations, which are instead very sensitive to the underlining description of the molecular structure. Here, we analyze the challenging case of the peridinin molecule, a natural apocarotenoid responsible for the light-harvesting process in the PCP antenna protein of dinoflagellates. Ground-state structural and vibrational properties, as well as electronic transitions of the pigment are studied by means of quantum-mechanical static and dynamic calculations. Thereafter, classical molecular dynamics simulations are performed with a number of different force-fields, ranging from a popular, general purpose one to refined potentials of increasing level of complexity. From the comparison of classical results with their quantum mechanical counterparts, it appears that, while very poor results are obtained from standard transferrable force-fields, specifically tuned potentials are able to correctly characterize most of the structural and vibrational features of the pigment. Nonetheless, only an advanced parametrization technique is able to give a semiquantitative description of the coupling between vibrations and electronic excitations, thus suggesting that the use of classical MD in combination of QM calculations for the study of photoinduced processes, albeit possible, should be considered with care.

We present an implicit solvation approach where the interface between the quantum-mechanical solute and the surrounding environment is described by a fully continuous permittivity built up with atomic-centered "soft" spheres. This approach combines many of the advantages of the self-consistent continuum solvation model in handling solutes and surfaces in contact with complex dielectric environments or electrolytes in electronic-structure calculations. In addition it is able to describe accurately both neutral and charged systems. The continuous function, describing the variation of the permittivity, allows to compute analytically the nonelectrostatic contributions to the solvation free energy that are described in terms of the quantum surface. The whole methodology is computationally stable, provides consistent energies and forces, and keeps the computational efforts and runtimes comparable to those of standard vacuum calculations. The capabilitiy to treat arbitrary molecular or slab-like geometries as well as charged molecules is key to tackle electrolytes within mixed explicit/implicit frameworks. We show that, with given, fixed atomic radii, two parameters are sufficient to give a mean absolute error of only 1.12 kcal/mol with respect to the experimental aqueous solvation energies for a set of 274 neutral solutes. For charged systems, the same set of parameters provides solvation energies for a set of 60 anions and 52 cations with an error of 2.96 and 2.13 kcal/mol, respectively, improving upon previous literature values. To tackle elements not present in most solvation databases, a new benchmark scheme on wettability and contact angles is proposed for solid-liquid interfaces and applied to the investigation of the stable terminations of a CdS (112̅0) surface in an electrochemical medium.

Hydrocarbon chains are important intermediates in various aqueous-phase surface processes, such as CO2 electroreduction, aqueous Fischer-Tropsch synthesis, and aqueous phase reforming of biomass-derived molecules. Further, the interaction between water and adsorbed hydrocarbons represents a difficult case for modern computational methods. Here, we explore various methods for calculating the energetics of this interaction within the framework of density functional theory and explore trade-offs between the use of low water coverages, molecular dynamics approaches, and minima hopping for identification of low energy structures. An effective methodology for simulating low temperature processes is provided by using a unit cell in which the vacuum space is filled with water, employing the minima hopping algorithm to search for low-lying minima, and including dispersion (van der Waals) interactions. Using this methodology, we show that a high coverage of adsorbed alkyls is destabilized by the presence of water, while a low coverage of alkyls is stabilized. Solvation has a small effect on the energetics of hydrocarbon chain growth, generally decreasing its favorability at low temperatures. We studied higher temperatures by running molecular dynamics simulations starting at the minima found by the minima hopping algorithm and found that increased temperatures facilitate chain growth. The self-consistent continuum solvation method effectively describes the alkyl-water interaction and is in general agreement with the explicit solvation results in most cases, but care should be taken at high alkyl coverage.

Carotenoids are important actors both in light-harvesting (LH) and in photoprotection functions of photosynthetic pigment-protein complexes. A deep theoretical investigation of this multiple role is still missing owing to the difficulty of describing the delicate interplay between electronic and nuclear degrees of freedom. A possible strategy is to combine accurate quantum mechanical (QM) methods with classical molecular dynamics. To do this, however, accurate force-fields (FF) are necessary. This article presents a new FF for the different carotenoids present in LH complexes of plants. The results show that all the important structural properties described by the new FF are in very good agreement with QM reference values. This increased accuracy in the simulation of the structural fluctuations is also reflected in the description of excited states. Both the energy order and the different nature of the lowest singlet states are preserved during the dynamics when the new FF is used, whereas an unphysical mixing is found when a standard FF is used., (© 2016 Wiley Periodicals, Inc.)

Plasmonic systems, such as metal nanoparticles, are becoming increasingly important in spectroscopies and devices because of their ability to enhance, even by several orders of magnitude, the photophysical properties of neighboring systems. In particular, it has been shown both theoretically and experimentally that combining nanoplasmonic devices with natural light-harvesting proteins substantially increases the fluorescence and absorption properties of the system. This kind of biohybrid device can have important applications in the characterization and design of efficient light-harvesting systems. In the present work, the FMO light-harvesting protein was combined with gold nanoparticles of different sizes, and its photophysical properties were characterized using a multiscale quantum-mechanical classical-polarizable and continuum model (QM/MMPol/PCM). By optimal tuning of the plasmon resonance of the metal nanoparticles, fluorescence enhancements of up to 2 orders of magnitude were observed. Orientation effects were found to be crucial: amplifications by factors of up to 300 were observed for the absorption process, while the radiative decay of the emitting state increased at most by a factor of 10, mostly as a result of poor alignment of the emitting state with the considered metal aggregates. Despite being a limiting factor for high-fluorescence-enhancement devices, the strong orientation dependence may represent an important feature of the natural light-harvesting system that could allow selective enhancement of a specific excited state of the complex.

Carotenoids are known to play a fundamental role in photosynthetic light-harvesting (LH) complexes; however, an accurate quantum-mechanical description of that is still missing. This is due to the multideterminant nature of the involved electronic states combined with an extended conjugation which limits the applicability of many of the most advanced approaches. In this study, we apply a multireference configuration interaction extension of density functional theory (DFT/MRCI) to describe transition energies and densities as well as the corresponding excitonic couplings, for the three lowest singlet excited states of nine carotenoids present in three different LH complexes of algae and plants. These benchmark results are used to find an approximated computational approach, which could be used to quantitatively reproduce the key quantities at a reduced computational cost. To this end, we tested the Tamm-Dancoff approximation (TDA) to time-dependent density functional theory in combination with different functionals. By analyzing the errors with respect to DFT/MRCI-TDA results for the full set of electronic properties, we conclude that TDA-TPSS with small basis sets indeed represents an effective approach to investigate LH processes that involve carotenoids.

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem and a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the Quantum ESPRESSO distribution of open-source codes.

Hydrogen fuel cells (FC) are considered essential for a sustainable economy based on carbon-free energy sources, but a major impediment are the costs. First-principles quantum mechanics (density functional theory including solvation) is used to predict how the energies and barriers for the mechanistic steps of the oxygen reduction reaction (ORR) over the fcc(111) platinum surface depend on the dielectric constant of the solvent. The ORR kinetics can be strongly accelerated by decreasing the effective medium polarizability from the high value it has in water. Possible ways to realize this experimentally are suggested. The calculated volcano structure for the dependence of rate on solvent polarization is considered to be general, and should be observed in other electrochemical systems., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

According to the amyloid cascade hypothesis, amyloid-β peptides (Aβ) play a causative role in Alzheimer's disease (AD), of which oligomeric forms are proposed to be the most neurotoxic by provoking oxidative stress. Copper ions seem to play an important role as they are bound to Aβ in amyloid plaques, a hallmark of AD. Moreover, Cu-Aβ complexes are able to catalyze the production of hydrogen peroxide and hydroxyl radicals, and oligomeric Cu-Aβ was reported to be more reactive. The flexibility of the unstructured Aβ peptide leads to the formation of a multitude of different forms of both Cu(I) and Cu(II) complexes. This raised the question of the structure-function relationship. We address this question for the biologically relevant Fenton-type reaction. Computational models for the Cu-Aβ complex in monomeric and dimeric forms were built, and their redox behavior was analyzed together with their reactivity with peroxide. A set of 16 configurations of Cu-Aβ was studied and the configurations were classified into 3 groups: (A) configurations that evolve into a linearly bound and nonreactive Cu(I) coordination; (B) reactive configurations without large reorganization between the two Cu redox states; and (C) reactive configurations with an open structure in the Cu(I)-Aβ coordination, which have high water accessibility to Cu. All the structures that showed high reactivity with H2O2 (to form HO(•)) fall into class C. This means that within all the possible configurations, only some pools are able to produce efficiently the deleterious HO(•), while the other pools are more inert. The characteristics of highly reactive configurations consist of a N-Cu(I)-N coordination with an angle far from 180° and high water crowding at the open side. This allows the side-on entrance of H2O2 and its cleavage to form a hydroxyl radical. Interestingly, the reactive Cu(I)-Aβ states originated mostly from the dimeric starting models, in agreement with the higher reactivity of oligomers. Our study gives a rationale for the Fenton-type reactivity of Cu-Aβ and how dimeric Cu-Aβ could lead to a higher reactivity. This opens a new therapeutic angle of attack against Cu-Aβ-based reactive oxygen species production.

Photosynthesis is triggered by the absorption of light by light-harvesting (LH) pigment-protein complexes followed by excitation energy transfer to the reaction center(s). A promising strategy to achieve control on and to improve light harvesting is to complement the LH complexes with plasmonic particles. Here a recently developed QM/MM/continuum approach is used to investigate the LH process of the peridinin-chlorophyll-protein (PCP) complex on a silver island film. The simulations not only reproduce and interpret the experiments but they also suggest general rules to design novel biohybrid devices; hot-spot configurations in which the LH complex is sandwiched between couples of metal aggregates are found to produce the largest amplifications. Indications about the best distances and orientations are also reported together with illumination and emission geometries of the PCP-NP system necessary to achieve the maximum enhancement.

Room-temperature ionic liquids (RTILs) have attracted much attention in the scientific community in the past decade due 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 calculations are reported. Here, in particular, 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 or the choice of the interaction potential, is analyzed in detail.

The solvation model proposed by Fattebert and Gygi [J. Comput. Chem. 23, 662 (2002)] and Scherlis et al. [J. Chem. Phys. 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 multigrid 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 [M. Cococcioni, F. Mauri, G. Ceder, and N. Marzari, Phys. Rev. Lett. 94, 145501 (2005)] of the solute. The resulting self-consistent continuum solvation 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 polarizable continuum 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., (© 2012 American Institute of Physics)

The structure of a water adlayer on a Pt(111) surface is investigated by means of extensive first-principles calculations. Allowing for proton disorder, the ground state energy for the [Formula: see text] structure can be found. This results from an interplay between water/metal chemical bonding and the hydrogen bonding of the water network. This picture is supported by substituting Pt(111) with Ag(111): the almost inert surface allows for the reconstruction of the hydrogen network.

In this work, we present an extension of a model previously proposed (Andreussi et al. J. Chem. Phys. 2004, 121, 10190) to treat the effect of a metal particle on the optical properties of a molecule in solution (close to such a particle) in the framework of the polarizable continuum model (PCM). This extension concerns the combination of such a model with the semiempirical method Zerner's intermediate neglect of differential overlap (ZINDO), which allows us to treat large size molecular systems, as the ones normally used in the experiments. A refinement of the model is also introduced to take into account the effect of the metal specimen on the absorption process of the molecular system, which affects the probability that a molecule reaches the excited state. Numerical tests are presented to validate the reliability of the ZINDO results with respect to quantum-mechanical DFT methods. Comparisons with experimental results on two different large molecular systems are reported, and the effect of the metal on the absorption process is discussed.

We present a model to evaluate the radiative and nonradiative lifetimes of electronic excited states of a molecule close to a metal particle of complex shape and, possibly, in the presence of a solvent. The molecule is treated quantum mechanically at Hartree-Fock (HF) or density-functional theory (DFT) level. The metal/solvent is considered as a continuous body, characterized by its frequency dependent local dielectric constant. For simple metal shapes (planar infinite surface and spherical particle) a version of the polarizable continuum model based on the integral equation formalism has been used, while an alternative methodology has been implemented to treat metal particles of arbitrary shape. In both cases, equations have been numerically solved using a boundary element method. Excitation energies and nonradiative decay rates due to the energy transfer from the molecule to the metal are evaluated exploiting the linear response theory (TDHF or TDDFT where TD--time dependent). The radiative decay rate of the whole system (molecule + metal/solvent) is calculated, still using a continuum model, in terms of the response of the surrounding to the molecular transition. The model presented has been applied to the study of the radiative and nonradiative lifetimes of a lissamine molecule in solution (water) and close to gold spherical nanoparticles of different radius. In addition, the influence of the metal shape has been analyzed by performing calculations on a system composed by a coumarin-type molecule close to silver aggregates of complex shape., (Copyright 2004 American Institute of Physics.)