Adsorption of Glycine on TiO2 in Water from On-the-fly Free-Energy Calculations and In Situ Electrochemical Impedance Spectroscopy.

We report here an experimental-computational study of hydrated TiO2 anatase nanoparticles interacting with glycine, where we obtain quantitative agreement of the measured adsorption free energies. Ab initio simulations are performed within the tight binding and density functional theory in combination with enhanced free-energy sampling techniques, which exploit the thermodynamic integration of the unbiased mean forces collected on-the-fly along the molecular dynamics trajectories. The experiments adopt a new and efficient setup for electrochemical impedance spectroscopy measurements based on portable screen-printed gold electrodes, which allows fast and in situ signal assessment. The measured adsorption free energy is -30 kJ/mol (both from experiment and calculation), with preferential interaction of the charged NH3+ group which strongly adsorbs on the TiO2 bridging oxygens. This highlights the importance of the terminal amino groups in the adsorption mechanism of amino acids on hydrated metal oxides. The excellent agreement between computation and experiment for this amino acid opens the doors to the exploration of the interaction free energies for other moderately complex bionano systems.

A Simple Electron-Density Based Force Field Model for High-Energy Interactions between Atoms and Molecules.

In high-energy molecular dynamics or Monte Carlo simulations, standard force fields optimized for simulations at ambient temperatures are inadequate. This is largely because their repulsive parts have been regarded as not very significant, even well below zero interaction energies. It is, therefore, not obvious which force fields to resort to for simulating hot gases or plasmas. A force field model that uses the electronic densities of noninteracting atoms or molecules within the pair approximation is introduced. We start by deriving a naïve model that neglects any exchange and correlation effects between the electronic clouds and then correct this model by adding a term calibrated from ab initio calculations using the CCSD(T)/cc-pVTZ level of theory. The resulting expression for this term can be regarded as a simple exchange-correlation function. We compare the results for the repulsive part of the potential energy hypersurfaces with the force fields commonly used on some dimers of small molecules.

A polarizable valence electron density based force field for high-energy interactions between atoms and molecules.

High-accuracy molecular force field models suited for hot gases and plasmas are not as abundant as those geared toward ambient pressure and temperature conditions. Here, we present an improved version of our previous electron-density based force field model that can now account for polarization effects by adjusting the atomic valence electron contributions to match ab initio calculated Mulliken partial charges. Using a slightly modified version of the Hohenberg-Kohn theorem, we also include an improved theoretical formulation of our model when applied to systems with degenerate ground states. We present two variants of our polarizable model, fitted from ab initio reference data calculated at CCSD(T)/cc-pVTZ and CCSD(T)/CEP-31G levels of theory, that both accurately model water dimer interaction energies. Further improvements include the additional interaction components with fictitious non-spherically symmetric, yet atom-centered, electron densities and fitting the exchange and correlation coefficients against analytical expressions. The latter removes all unphysical oscillations that are observed in the previous non-polarizable variant of our force field.

Toward an efficient f-in-core/f-in-valence switchable description for DFTB calculations of Ce 4f states in ceria.

A computational protocol is developed for efficient studies of partially reduced redox-active oxides using the self-consistent charge density functional tight-binding method. The protocol is demonstrated for ceria, which is a prototypical reducible oxide material. The underlying idea is to achieve a consistent (and harmonized) set of Slater-Koster (SK) tables with connected repulsive potentials that enable switching on and off the in-valence description of the Ce 4f states without serious loss of accuracy in structure and energetics. The implicit treatment of the Ce 4f states, with the use of f-in-core SK-tables, is found to lead to a significant decrease in computational time. More importantly, it allows for explicit control of the oxidation states of individual Ce atoms. This makes it possible to "freeze" the electronic configuration, thereby allowing the exploration of the energetics for various meta-stable configurations. We anticipate that the outlined strategy can help to shed light on the interplay between the size, shape, and redox activity for nanoceria and other related materials.

Water on ceria{111}: Comparison between 23 experimental vibrational studies in the literature and new modeling.

Theoretical and experimental vibrational signatures of H2O and OH- (dissociated water) adsorbed on stoichiometric ceria{111} surfaces are compared. The experimental ones were collected from low-coverage experiments in the literature, and the theoretical anharmonic frequencies were generated using density functional theory calculations employing the optPBE-vdW functional for coverages from 0.5 to a few monolayers. It is found that (i) the experiments and our calculations overall agree well, lending credibility to both; (ii) the calculations manage to resolve the large class of H-bonded motifs into frequency classes that can guide experimental assignments; (iii) it is possible to find a geometrical H-bond definition that also captures the OH vibrational frequency downshifts well: R(H⋯O) ≤2.5 Å and the O-H⋯O angle θ ≥ 100°; and (iv) the frequency vs electric field relations for water and hydroxides (i.e., dissociated water) follow different and well-separated curves.

H2O2(s) and H2O2·2H2O(s) crystals compared with ices: DFT functional assessment and D3 analysis.

The H2O and H2O2 molecules resemble each other in a multitude of ways as has been noted in the literature. Here, we present density functional theory (DFT) calculations for the H2O2(s) and H2O2·2H2O(s) crystals and make selected comparisons with ice polymorphs. The performance of a number of dispersion-corrected density functionals-both self-consistent and a posteriori ones-are assessed, and we give special attention to the D3 correction and its effects. The D3 correction to the lattice energies is large: for H2O2(s) the D3 correction constitutes about 25% of the lattice energy using PBE, much more for RPBE, much less for SCAN, and it primarily arises from non-H-bonded interactions out to about 5 Å.The large D3 corrections to the lattice energies are likely a consequence of several effects: correction for missing dispersion interaction, the ability of D3 to capture and correct various other kinds of limitations built into the underlying DFT functionals, and finally some degree of cell-contraction-induced polarization enhancement. We find that the overall best-performing functionals of the twelve examined are optPBEvdW and RPBE-D3. Comparisons with DFT assessments for ices in the literature show that where the same methods have been used, the assessments largely agree.

Origin of the Hydrophobic Behaviour of Hydrophilic CeO2.

The nature of the hydrophobicity found in rare-earth oxides is intriguing. The CeO2 (100) surface, despite its strongly hydrophilic nature, exhibits hydrophobic behaviour when immersed in water. In order to understand this puzzling and counter-intuitive effect we performed a detailed analysis of the confined water structure and dynamics. We report here an ab-initio molecular dynamics simulation (AIMD) study which demonstrates that the first adsorbed water layer, in immediate contact with the hydroxylated CeO2 surface, generates a hydrophobic interface with respect to the rest of the liquid water. The hydrophobicity is manifested in several ways: a considerable diffusion enhancement of the confined liquid water as compared with bulk water at the same thermodynamic condition, a weak adhesion energy and few H-bonds above the hydrophobic water layer, which may also sustain a water droplet. These findings introduce a new concept in water/rare-earth oxide interfaces: hydrophobicity mediated by specific water patterns on a hydrophilic surface.

Vertical-Flow Paper Sensor for On-Site and Prompt Evaluation of Chloride Contamination in Concrete Structures.

Corrosion occurring in reinforced concrete has turned into a primary concern of the current century, concrete being the most ubiquitous and predominant material used in the construction industry. Among the many interrelated processes that trigger corrosion of metallic reinforcements, the penetration of chloride ions into the concrete matrix is the most insidious threat. Herein, we developed the first electrochemical device entirely made of paper that allows for the direct, prompt, and noninvasive evaluation of free chloride ion contamination in concrete-based constructions. Our device is based on a three-layer wax-modified filter paper, consisting of two Ag/AgCl screen-printed electrodes that are interfaced by a junction pad in a sandwich-like configuration. Filter paper allows for generating a vertical-flow potentiometric device capable of measuring the electrochemical potential between two solutions containing different concentrations of chloride ions, which are separately drop-cast on the top and bottom layers. After demonstrating the analytical performance of the device, the same principle was applied to the evaluation of the chloride contents in different concrete samples, exploiting paper as a suitable interfacing material for potentiometric measurements on the cement solid surface. Laboratory-prepared concrete samples with known chloride contents were first assessed, and then, the paper-based vertical-flow device was applied to real concrete structures at the Giacomo Manzù Museum (Ardea, Italy) for the evaluation of chloride contamination caused by the proximity to the seaside. The capability of our device to provide timely warning of the risk conditions of concrete-based artifacts was demonstrated.

Oxygen chemistry of halogen-doped CeO2(111).

We study substitutional fluorine, chlorine and bromine impurities at CeO2(111), and their effects on the oxygen chemistry of the surface, using density functional theory. We find that impurity formation results in a halide ion and one Ce3+ ion for all three halogens, although the formation energy depends strongly on the identity of the halogen; however, once formed, all three halogens exhibit a similar propensity to form impurity-impurity pairs. Furthermore, while the effects of halogen impurities on oxygen vacancy formation are marginal, they are more significant for oxygen molecule adsorption, due to electron transfer from the Ce3+ ion which results in an adsorbed superoxide molecule. We also consider the displacement of a halide ion on to the surface by half of an oxygen molecule, and find that the energy required to do so depends strongly not only on the identity of the halogen, but also on whether or not a second halogen impurity, with its associated Ce3+ ion, is present; if it is, then the process is greatly facilitated. Overall, our results demonstrate the existence of a rich variety of ways in which the oxygen chemistry of CeO2(111) may be modified by the presence of halogen dopants.

Supercooled liquid-like dynamics in water near a fully hydrated titania surface: Decoupling of rotational and translational diffusion.

We report an ab initio molecular dynamics (MD) simulation investigating the effect of a fully hydrated surface of TiO2 on the water dynamics. It is found that the universal relation between the rotational and translational diffusion characteristics of bulk water is broken in the water layers near the surface with the rotational diffusion demonstrating progressive retardation relative to the translational diffusion when approaching the surface. This kind of rotation-translation decoupling has so far only been observed in the supercooled liquids approaching glass transition, and its observation in water at a normal liquid temperature is of conceptual interest. This finding is also of interest for the application-significant studies of the water interaction with fully hydrated nanoparticles. We note that this is the first observation of rotation-translation decoupling in an ab initio MD simulation of water.

Temperature effects on the ionic conductivity in concentrated alkaline electrolyte solutions.

Alkaline electrolyte solutions are important components in rechargeable batteries and alkaline fuel cells. As the ionic conductivity is thought to be a limiting factor in the performance of these devices, which are often operated at elevated temperatures, its temperature dependence is of significant interest. Here we use NaOH as a prototypical example of alkaline electrolytes, and for this system we have carried out reactive molecular dynamics simulations with an experimentally verified high-dimensional neural network potential derived from density-functional theory calculations. It is found that in concentrated NaOH solutions elevated temperatures enhance both the contributions of proton transfer to the ionic conductivity and deviations from the Nernst-Einstein relation. These findings are expected to be of practical relevance for electrochemical devices based on alkaline electrolyte solutions.

The water/ceria(111) interface: Computational overview and new structures.

Thin film structures of water on the CeO2(111) surface for coverages between 0.5 and 2.0 water monolayers have been optimized and analyzed using density functional theory (optPBE-vdW functional). We present a new 1.0 ML structure that is both the lowest in energy published and features a hydrogen-bond network extending the surface in one-dimension, contrary to what has been found in the literature, and contrary to what has been expected due to the large bulk ceria cell dimension. The adsorption energies for the monolayer and multilayered water structures agree well with experimental temperature programmed desorption results from the literature, and we discuss the stability window of CeO2(111) surfaces covered with 0.5-2.0 ML of water.

Anion-mediated electronic effects in reducible oxides: Tuning the valence band of ceria via fluorine doping.

Combining experimental spectroscopy and hybrid density functional theory calculations, we show that the incorporation of fluoride ions into a prototypical reducible oxide surface, namely, ceria(111), can induce a variety of nontrivial changes to the local electronic structure, beyond the expected increase in the number of Ce3+ ions. Our resonant photoemission spectroscopy results reveal new states above, within, and below the valence band, which are unique to the presence of fluoride ions at the surface. With the help of hybrid density functional calculations, we show that the different states arise from fluoride ions in different atomic layers in the near surface region. In particular, we identify a structure in which a fluoride ion substitutes for an oxygen ion at the surface, with a second fluoride ion on top of a surface Ce4+ ion giving rise to F 2p states which overlap the top of the O 2p band. The nature of this adsorbate F--Ce4+ resonant enhancement feature suggests that this bond is at least partially covalent. Our results demonstrate the versatility of anion doping as a potential means of tuning the valence band electronic structure of ceria.

Red-shifting and blue-shifting OH groups on metal oxide surfaces - towards a unified picture.

We analyse the OH vibrational signatures of 56 structurally unique water molecules and 34 structurally unique hydroxide ions in thin water films on MgO(001) and CaO(001), using DFT-generated anharmonic potential energy surfaces. We find that the OH stretching frequencies of intact water molecules on the surface are always downshifted with respect to the gas-phase species while the OH- groups are either upshifted or downshifted. Despite these differences, the main characteristics of the frequency shifts for all three types of surface OH groups (OHw, OsH and OHf) can be accounted for by one unified expression involving the in situ electric field from the surrounding environment, and the gas-phase molecular properties of the vibrating species (H2O or OH-). The origin behind the different red- and blueshift behaviour can be traced back to the fact that the molecular dipole moment of a gas-phase water molecule increases when an OH bond is stretched, but the opposite is true for the hydroxide ion. We propose that familiarity with the relations presented here will help surface scientists in the interpretation of vibrational OH spectra for thin water films on ionic crystal surfaces.

Maximally resolved anharmonic OH vibrational spectrum of the water/ZnO(101¯0) interface from a high-dimensional neural network potential.

Unraveling the atomistic details of solid/liquid interfaces, e.g., by means of vibrational spectroscopy, is of vital importance in numerous applications, from electrochemistry to heterogeneous catalysis. Water-oxide interfaces represent a formidable challenge because a large variety of molecular and dissociated water species are present at the surface. Here, we present a comprehensive theoretical analysis of the anharmonic OH stretching vibrations at the water/ZnO(101¯0) interface as a prototypical case. Molecular dynamics simulations employing a reactive high-dimensional neural network potential based on density functional theory calculations have been used to sample the interfacial structures. In the second step, one-dimensional potential energy curves have been generated for a large number of configurations to solve the nuclear Schrödinger equation. We find that (i) the ZnO surface gives rise to OH frequency shifts up to a distance of about 4 Å from the surface; (ii) the spectrum contains a number of overlapping signals arising from different chemical species, with the frequencies decreasing in the order ν(adsorbed hydroxide) > ν(non-adsorbed water) > ν(surface hydroxide) > ν(adsorbed water); (iii) stretching frequencies are strongly influenced by the hydrogen bond pattern of these interfacial species. Finally, we have been able to identify substantial correlations between the stretching frequencies and hydrogen bond lengths for all species.

Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations.

Zinc plays important roles in structural stabilization of proteins, enzyme catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynamics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Drude polarizable force field agreed better with the ab initio results, although the deviations between QM and MM were still rather large (40-96 kcal/mol). In order to gain further insight into Zn-ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand-ligand interactions did not play a significant role in the binding of Zn. Finally, analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn binding dynamics. An exchange between carboxylate (Asp/Glu) and imidazole (His) is less likely.

Fluorine impurities at CeO2(111): Effects on oxygen vacancy formation, molecular adsorption, and surface re-oxidation.

We investigate the effects of anion doping with fluorine impurities on the chemistry of the CeO2 (111) facet, using the results of DFT + U calculations. We consider three prototypical processes: the formation of oxygen vacancies, the adsorption of O2 and H2O molecules, and the re-oxidation of the surface with fragments of the two molecules. We find that the first two of these processes are not strongly affected, but that the presence of F lowers the energy gained in the re-oxidation of the surface in comparison to the healing of an oxygen vacancy, by 1.47 eV in the case of O2 (provided that the F is part of a cluster) and by 0.92 eV in the case of H2O. Based on these results, we suggest that F could enhance the redox chemistry of ceria by toggling between being in the surface and on the surface, effectively facilitating the release of lattice O by acting as a "place holder" for it. Finally, we find that the desorption of F as either 12F2 or HF is energetically unfavourable, suggesting that F doped ceria should be stable in the presence of O2 and H2O.

Comparing van der Waals DFT methods for water on NaCl(001) and MgO(001).

In this work, a range of van der Waals type density functionals are applied to the H2O/NaCl(001) and H2O/MgO(001) interface systems to explore the effect of an explicit dispersion treatment. The functionals we use are the self-consistent vdW functionals vdW-DF, vdW-DF2, optPBE-vdW, optB88-vdW, optB86b-vdW, and vdW-DF-cx, as well as the dispersion-corrected PBE-TS and PBE-D2 methods; they are all compared with the standard PBE functional. For both NaCl(001) and MgO(001), we find that the dispersion-flavoured functionals stabilize the water-surface interface by approximately 20%-40% compared to the PBE results. For NaCl(001), where the water molecules remain intact for all overlayers, the dominant contribution to the adsorption energy from "density functional theory dispersion" stems from the water-surface interactions rather than the water-water interactions. The optPBE-vdW and vdW-DF-cx functionals yield adsorption energies in good agreement with available experimental values for both NaCl and MgO. To probe the strengths of the perturbations of the adsorbed water molecules, we also calculated water dipole moments and found an increase up to 85% for water at the MgO(001) surface and 70% at the NaCl(001) surface, compared to the gas-phase dipole moment.

Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10(1)0).

We assess the consequences of the interface model-embedded-cluster or periodic-slab model-on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic-slab calculations indicate a delocalized charge-transfer state. Our example is Cu atom adsorption on ZnO(10(1)0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded-cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom-centered and plane-waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10(1)0), as long as care is taken to account for the effects of CT.

Vibrational models for a crystal with 36 water molecules in the unit cell: IR spectra from experiment and calculation.

We present experimental and calculated IR spectra of the water molecules in crystalline aluminium nitrate nonahydrate and a method to generate a realistic and well resolved isotope-isolated spectrum from periodic DFT calculations. Our sample crystal contains 18 structurally different OH groups and is a perfect benchmark compound to validate vibrational models and the structure-property relationship of bound water molecules. FTIR spectra (ATR technique) were recorded for the Al(NO3)3·9H2O crystal at 138 and 298 K, and due to a multitude of OH contributions and couplings, they are naturally poorly resolved and yield a broad OH band in the range 3500 to 2700 cm(-1) at both temperatures. Isotope-isolated IR spectra have the clear advantage over non-deuterated spectra that they are better resolved and easier to interpret - here we have extended the experimental study by simulating the isotope-isolated IR spectrum, using PBE-D2 and auxiliary B3LYP calculations and an anharmonic OH vibrational model. We find excellent agreement between the shapes and frequency ranges of the experimental and calculated OH spectral bands. We make use of four different vibrational models: (i) a harmonic lattice-dynamical model for the isotope-isolated crystal with 1 H among 71 D, (ii) a harmonic lattice-dynamical model for the normal undeuterated crystal involving all the vibrational couplings, (iii) a harmonic 1-dimensional uncoupled OH vibrational model, and (iv) the anharmonic variant of the previous model, which yields the final spectrum. We also use the individual frequencies, resolved by the calculations, to quantify new or extended relationships involving OH frequencies versus local electric fields and H-bond distances. We explore the correlation between OH frequency and molecular dipole moment for bound water molecules.