DFT2FEFFIT: a density-functional-theory-based structural toolkit to analyze EXAFS spectra.

This article presents a Python-based program, DFT2FEFFIT, to regress theoretical extended X-ray absorption fine structure (EXAFS) spectra calculated from density functional theory structure models against experimental EXAFS spectra. To showcase its application, Ce-doped fluorapatite [Ca10(PO4)6F2] is revisited as a representative of a material difficult to analyze by conventional multi-shell least-squares fitting of EXAFS spectra. The software is open source and publicly available.

Unraveling the Oxidation Kinetics Through Electronic Structure Regulation of MnCo2O4.5@Ni3S2 p-n Junction for Urea-Assisted Electrocatalytic Activity.

A promising strategy to boost electrocatalytic performance is via assembly of hetero-nanostructured electrocatalysts that delivers the essential specific surface area and also active sites by lowering the reaction barrier. However, the challenges associated with the intricate designs and mechanisms remain underexplored. Therefore, the present study constructs a p-n junction in a free-standing MnCo2O4.5@Ni3S2 on Ni-Foam. The space-charge region's electrical characteristics is dramatically altered by the formed p-n junction, which enhances the electron transfer process for urea-assisted electrocatalytic water splitting (UOR). The optimal MnCo2O4.5@Ni3S2 electrocatalyst results in greater oxygen evolution reactivity (OER) than pure systems, delivering an overpotential of only 240 mV. Remarkably, upon employing as UOR electrode the required potential decreases to 30 mV. The impressive performance of the designed catalyst is attributed to the enhanced electrical conductivity, greater number of electrochemical active sites, and improved redox activity due to the junction interface formed between p-MnCo2O4.5 and n-Ni3S2. There are strong indications that the in situ formed extreme-surface NiOOH, starting from Ni3S2, boosts the electrocatalytic activity, i.e., the electrochemical  surface reconstruction generates the active species. In conclusion, this work presents a high-performance p-n junction design for broad use, together with a viable and affordable UOR electrocatalyst.

Modeling the polychromism of oxide minerals: The case of alexandrite and cordierite.

In this work, we investigate the spectroscopic properties of photochromic alexandrite and cordierite by TD-DFT. The objective is to assess the TD-DFT for the simulation of pleochroism (change of color depending on the crystallographic direction of the observation) and the change of color as a function of the light source. For these simulations, we compared an embedding where dangling bonds are saturated by hydrogen atoms and an electrostatic embedding. The electrostatic embedding provided numerically more stable results and allowed a good reproduction of the pleochroism of cordierite, based on a Fe2+-Fe3+ intervalence charge transfer transition. However, the pleochroism of alexandrite is not as well reproduced, suggesting that TD-DFT has some difficulties to reproduce the anisotropy of the transition dipole moment, an aspect that is not deeply documented in the literature.

Gaussian attractive potential for carboxylate/cobalt surface interactions.

Ligand-decorated metal surfaces play a pivotal role in various areas of chemistry, particularly in selective catalysis. Molecular dynamics simulations at the molecular mechanics level of theory are best adapted to gain complementary insights to experiments regarding the structure and dynamics of such organic films. However, standard force fields tend to capture only weak physisorption interactions. This is inadequate for ligands that are strongly adsorbed such as carboxylates on metal surfaces. To address this limitation, we employ the Gaussian Lennard-Jones (GLJ) potential, which incorporates an attractive Gaussian potential between the surface and ligand atoms. Here, we develop this approach for the interaction between cobalt surfaces and carboxylate ligands. The accuracy of the GLJ approach is validated through the analysis of the interaction of oxygen with two distinct cobalt surfaces. The accuracy of this method reaches a root mean square deviation (RMSD) of about 3 kcal/mol across all probed configurations, which corresponds to a percentage error of roughly 4%. Application of the GLJ force field to the dynamics of the organic layer on these surfaces reveals how the ligand concentration influences the film order, and highlights differing mobility in the x and y directions, attributable to surface corrugation on Co(112̄0). GLJ is versatile, suitable for a broad range of metal/ligand systems, and can, subsequently, be utilized to study the organic film on the adsorption/desorption of reactants and products during a catalytic process.

One-Step Electrocatalytic Approach Applied to the Synthesis of ß-Propiolactones from CO2 and Dienes.

ß-Lactones are common substructures in a variety of natural products and drugs, and they serve as versatile synthetic intermediates in the production of valuable chemical derivatives. Traditional ß-lactone synthesis relies on laborious multi-step synthetic methods that use toxic compounds, sophisticated catalysts, expensive, and/or reactive chemicals. Based on the in situ electrochemical formation of metal-based nanoclusters, this paper describes the development of a one-step, room temperature electrocatalytic method for the formation of stable ß-lactone from CO2 and dienes. This one-step "electrosynthesis" method results in the formation of a new class of ß-lactone with high selectivity (up to 100%) and activity (up to 80% yields with respect to the reacted diene) by regulating the applied potential and current density. This work paves the way for more sustainable and environmentally friendly reaction pathways based on the in situ formation of nanoclusters as organic electrosynthesis catalysts.

An Electrostatically Embedded QM/MM Scheme for Electrified Interfaces.

Atomistic modeling of electrified interfaces remains a major issue for detailed insights in electrocatalysis, corrosion, electrodeposition, batteries, and related devices such as pseudocapacitors. In these domains, the use of grand-canonical density functional theory (GC-DFT) in combination with implicit solvation models has become popular. GC-DFT can be conveniently applied not only to metallic surfaces but also to semiconducting oxides and sulfides and is, furthermore, sufficiently robust to achieve a consistent description of reaction pathways. However, the accuracy of implicit solvation models for solvation effects at interfaces is in general unknown. One promising way to overcome the limitations of implicit solvents is going toward hybrid quantum mechanical (QM)/molecular mechanics (MM) models. For capturing the electrochemical potential dependence, the key quantity is the capacitance, i.e., the relation between the surface charge and the electrochemical potential. In order to retrieve the electrochemical potential from a QM/MM hybrid scheme, an electrostatic embedding is required. Furthermore, the charge of the surface and of the solvent regions has to be strictly opposite in order to consistently simulate charge-neutral unit cells in MM and in QM. To achieve such a QM/MM scheme, we present the implementation of electrostatic embedding in the VASP code. This scheme is broadly applicable to any neutral or charged solid/liquid interface. Here, we demonstrate its use in the context of GC-DFT for the hydrogen evolution reaction (HER) over a noble-metal-free electrocatalyst, MoS2. We investigate the effect of electrostatic embedding compared to the implicit solvent model for three contrasting active sites on MoS2: (i) the sulfur vacancy defect, which is rather apolar; (ii) a Mo antisite defect, where the active site is a surface bound highly polar OH group; and (iii) a reconstructed edge site, which is generally believed to be responsible for most of the catalytic activity. According to our results, the electrostatic embedding leads to almost indistinguishable results compared to the implicit solvent for the apolar system but has a significant effect on polar sites. This demonstrates the reliability of the hybrid QM/MM, electrostatically embedded solvation model for electrified interfaces.

Toward a Realistic Surface State of Ru in Aqueous and Gaseous Environments.

Identifying the surface species is critical in developing a realistic understanding of supported metal catalysts working in water. To this end, we have characterized the surface species present at a Ru/water interface by employing a hybrid computational approach involving an explicit description of the liquid water and a possible pressure of H2. On the close-packed, most stable Ru(0001) facet, the solvation tends to favor the full dissociation of water into atomic O and H in contrast with the partially dissociated water layer reported for ultra-high-vacuum conditions. The solvation stabilization was found to reach -0.279 J m2, which results in stable O and H species on Ru(0001) in the presence of liquid water even at room temperature. Conversely, introducing even a small H2 pressure (10-2 bar) results in a monolayer of chemisorbed H at the interface, a general trend found on the three most exposed facets of Ru nanoparticles. While hydroxyls were often hypothesized as possible surface species at the Ru/water interface, this computational study clearly demonstrates that they are not stabilized by liquid water and are not found under realistic reductive catalytic conditions.

How machine learning can accelerate electrocatalysis discovery and optimization.

Advances in machine learning (ML) provide the means to bypass bottlenecks in the discovery of new electrocatalysts using traditional approaches. In this review, we highlight the currently achieved work in ML-accelerated discovery and optimization of electrocatalysts via a tight collaboration between computational models and experiments. First, the applicability of available methods for constructing machine-learned potentials (MLPs), which provide accurate energies and forces for atomistic simulations, are discussed. Meanwhile, the current challenges for MLPs in the context of electrocatalysis are highlighted. Then, we review the recent progress in predicting catalytic activities using surrogate models, including microkinetic simulations and more global proxies thereof. Several typical applications of using ML to rationalize thermodynamic proxies and predict the adsorption and activation energies are also discussed. Next, recent developments of ML-assisted experiments for catalyst characterization, synthesis optimization and reaction condition optimization are illustrated. In particular, the applications in ML-enhanced spectra analysis and the use of ML to interpret experimental kinetic data are highlighted. Additionally, we also show how robotics are applied to high-throughput synthesis, characterization and testing of electrocatalysts to accelerate the materials exploration process and how this equipment can be assembled into self-driven laboratories.

Beyond single-crystal surfaces: The GAL21 water/metal force field.

Solvent effects are notoriously difficult to describe for metallic nanoparticles (NPs). Here, we introduce GAL21 which is the first pairwise additive force field that is specifically designed to modulate the near chemisorption energy of water as a function of the coordination numbers of the metallic atoms. We find a quadratic dependence to be most suitable for capturing the dependence of the adsorption energy of water on the generalized coordination number (GCN) of the metal atoms. GAL21 has been fitted against DFT adsorption energies for Cu, Ag, Au, Ni, Pd, Pt, and Co on 500 configurations and validated on about 3000 configurations for each metal, constructed on five surfaces with GCNs varying from 2.5 to 11.25. Depending on the metals, the root mean square deviation is found between 0.7 kcal mol-1 (Au) to 1.6 kcal mol-1 (Ni). Using GAL21, as implemented in the open-source code CP2K, we then evaluate the solvation energy of Au55 and Pt55 NPs in water using thermodynamic integration. The solvation free energy is found to be larger for Pt than for Au and systematically larger than 200 kcal mol-1, demonstrating the large impact of solvent on the surface energetics of NPs. Still, given that the amorphous NPs are both, the most stable and the most solvated ones, we do not predict a change in the preferred morphology between the gas-phase and in water. Finally, based on a linear regression on three sizes of NPs (from 38 to 147), the solvation energy for Au and Pt surface atoms is found to be -5.2 and -9.9 kcal mol-1, respectively.

Modeling Electrochemical Processes with Grand Canonical Treatment of Many-Body Perturbation Theory.

Electrocatalysis plays a key role in sustainable energy conversion and storage. It is critical to model the grand canonical treatment of electrons, which accounts for the electrochemical potential explicitly, at the atomic scale and understand these reactions at electrified interfaces. However, such a grand canonical treatment for electrocatalytic modeling is in practice restricted to a treatment of electronic structure with density functional theory, and more accurate methods are in many cases desirable. Here, we develop an original workflow combining the grand canonical treatment of electrons with many-body perturbation theory in its random phase approximation (RPA). Using the potential dependent adsorption of carbon monoxide on the copper (100) facet, we show that the grand canonical RPA energetics provide the correct on-top Cu geometry for CO at reducing potential. The match with experimental results is significantly improved compared to the functionals at the generalized gradient approximation level, which is the most commonly used approximation for electrochemical applications. We expect this development to pave the way to further electrochemical applications using RPA.

Same ligand, three first-row metals: comparing M-amido bifunctional reactivity (Mn, Fe, Co).

The bifunctional reactivity of three metal SNS (bis)amido complexes was computationally assessed by comparing the nucleophilicity of the M-Namido donor (Mn, Fe, Co). Hirshfeld charges identified the Mn-Namido donor as most nucleophilic and Fe as most electrophilic metal. Reaction energy profiles of a model bifunctional H2 activation showed Mn with the lowest reaction barrier (17 kcal mol-1), followed by Fe and Co (21 and 29 kcal mol-1).

Transferable Gaussian Attractive Potentials for Organic/Oxide Interfaces.

Organic/oxide interfaces play an important role in many areas of chemistry and in particular for lubrication and corrosion. Molecular dynamics simulations are the method of choice for providing complementary insight to experiments. However, the force fields used to simulate the interaction between molecules and oxide surfaces tend to capture only weak physisorption interactions, discarding the stabilizing Lewis acid/base interactions. We here propose a simple complement to the straightforward molecular mechanics description based on "out-of-the-box" Lennard-Jones potentials and electrostatic interactions: the addition of an attractive Gaussian potential between reactive sites of the surface and heteroatoms of adsorbed organic molecules, leading to the Gaussian Lennard-Jones (GLJ) potential. The interactions of four oxygenated and four amine molecules with the typical and widespread hematite and γ-alumina surfaces are investigated. The root mean square deviation (RMSD) for all probed molecules is only 5.7 kcal/mol, which corresponds to an error of 23% over hematite. On γ-alumina, the RMSD is 11.2 kcal/mol using a single parameter for all five chemically inequivalent surface aluminum atoms. Applying GLJ to the simulation of organic films on oxide surfaces demonstrates that the mobility of the surfactants is overestimated by the simplistic LJ potential, while GLJ and other qualitatively correct potentials show a strong structuration and slow dynamics of the surface films, as could be expected from the first-principles adsorption energies for model head groups.

DockOnSurf: A Python Code for the High-Throughput Screening of Flexible Molecules Adsorbed on Surfaces.

We present the open-source python package DockOnSurf which automates the generation and optimization of low-energy adsorption configurations of molecules on extended surfaces and nanoparticles. DockOnSurf is especially geared toward handling polyfunctional flexible adsorbates. The use of this high-throughput workflow allows us to carry out the screening of adsorbate-surface configurations in a systematic, customizable, and traceable way, while keeping the focus on the chemically relevant structures. The screening strategy consists in splitting the exploration of the adsorbate-surface configurational space into chemically meaningful domains, that is, by choosing among different conformers to adsorb, surface adsorption sites, adsorbate anchoring points, and orientations and allowing dissociation of (acidic) protons. We demonstrate the performance of the main features based on varying examples, ranging from CO adsorption on a gold nanoparticle to sorbitol adsorption on hematite. Through the use of the presented program, we aim to foster efficiency, traceability, and ease of use in research within tribology, catalysis, nanoscience, and surface science in general.

(Dis)Similarities of adsorption of diverse functional groups over alumina and hematite depending on the surface state.

To accelerate the conversion to more sustainable lubricants, there is a need for an improved understanding of the adsorption at the solid/liquid interface. As a first step, the density functional theory computed adsorption energies can be used to screen the ability of additives to cover a surface. Analogously to what has been found in catalysis with the universal scaling relations, we investigate here if a general universal ranking of additives can be found, independently of the surface considered. We divided our set of 25 diverse representative molecules into aprotic and protic molecules. We compared their adsorption over alumina and hematite, which are models of surface oxidized aluminum and steel, respectively. The adsorption energy ranking of our set is not strongly affected by alumina hydration. In contrast, adsorption on hematite is more strongly affected by hydration since all exposed Fe Lewis acid sites are converted into hydroxylated Brønsted basic sites. However, the ranking obtained on hydrated hematite is close to the one obtained on dry alumina, paving the road to a fast screening of additives. In our library, protic molecules are more strongly adsorbed than non-protic molecules. In particular, methyl and dimethyl phosphates are the most strongly adsorbed ones, followed by N-methyldiethanolamine, succinimide, and ethanoic acid. Additives combining these functional groups are expected to strongly adsorb at the solid/liquid interface and, therefore, likely to be relevant components of lubricant formulations.

The Impact of Water on Ru-Catalyzed Olefin Metathesis: Potent Deactivating Effects Even at Low Water Concentrations.

Ruthenium catalysts for olefin metathesis are widely viewed as water-tolerant. Evidence is presented, however, that even low concentrations of water cause catalyst decomposition, severely degrading yields. Of 11 catalysts studied, fast-initiating examples (e.g., the Grela catalyst RuCl2(H2IMes)(=CHC6H4-2-O i Pr-5-NO2) were most affected. Maximum water tolerance was exhibited by slowly initiating iodide and cyclic (alkyl)(amino)carbene (CAAC) derivatives. Computational investigations indicated that hydrogen bonding of water to substrate can also play a role, by retarding cyclization relative to decomposition. These results have important implications for olefin metathesis in organic media, where water is a ubiquitous contaminant, and for aqueous metathesis, which currently requires superstoichiometric "catalyst" for demanding reactions.

What does graphitic carbon nitride really look like?

Graphitic carbon nitrides (g-CNs) have become popular light absorbers in photocatalytic water splitting cells. Early theoretical work on these structures focused on fully polymerized g-C3N4. Experimentally, it is known that the typically employed melamine polycondensation does not go toward completion, yielding structures with ∼15 at% hydrogen. Here, we study the conformational stability of "melon", with the [C6N9H3]n structural formula using DFT. Referencing to a 2D melon sheet, B3LYP-dDsC and PBE-MBD computations revealed the same qualitative trend in stability of the 3D structures, with several of them within 5 kJ mol-1 per tecton. Fina's orthorhombic melon is the most stable of the studied conformers, with Lotsch' monoclinic melon taking an intermediate value. Invoking a simple Wannier-Mott-type approach, Fina's and Lotsch' structures exhibited the lowest optical gaps (2.8 eV), within the error margin of the experimental value (2.7 eV). All conformers yielded gaps below that of the monolayer's (3.2 eV), suggesting Jelley-type ("J") aggregation effects.

Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid Quantum-Mechanical/Molecular Mechanics Simulations.

Modeling adsorption at metal/water interfaces is a cornerstone toward an improved understanding in a variety of fields from heterogeneous catalysis to corrosion. We propose and validate a hybrid scheme that combines the adsorption free energies obtained in the gas phase at the density functional theory level with the variation in solvation from the bulk phase to the interface evaluated using a MM-based alchemical transformation, denoted MMsolv. Using the GAL17 force field for the platinum/water interaction, we retrieve a qualitatively correct interaction energy of the water solvent at the interface. This interaction is of near chemisorption character and thus challenging, both for the alchemical transformation and also for the fixed point-charge electrostatics. Our scheme passes through a state characterized by a well-behaved physisorption potential for the Pt(111)/H2O interaction to converge the free energy difference. The workflow is implemented in the freely available SolvHybrid package. We first assess the adsorption of a water molecule at the Pt/water interface, which turns out to be a stringent test. The intrinsic error of our quantum-mechanical/molecular mechanics (QM/MM) hybrid scheme is limited to 6 kcal mol-1 through the introduction of a correction term to attenuate the electrostatic interaction between near-chemisorbed water molecules and the underlying Pt atoms. Next, we show that the MMsolv solvation free energy of Pt (-0.46 J m-2) is in good agreement with the experimental estimate (-0.32 J m-2). Furthermore, we show that the entropy contribution at room temperature is roughly of equal magnitude as the free energy but with an opposite sign. Finally, we compute the adsorption energy of benzene and phenol at the Pt(111)/water interface, one of the rare systems for which experimental data are available. In qualitative agreement with the experiment, but in stark contrast with a standard implicit solvent model, the adsorption of these aromatic molecules is strongly reduced (i.e., less exothermic by ∼30 and 40 kcal mol-1 for our QM/MM hybrid scheme and experiment, respectively, but ∼0 with the implicit solvent) at the solid/liquid interface compared to the solid/gas interface. This reduction occurs mainly because of the competition between the organic adsorbate and the solvent for adsorption on the metallic surface. The semiquantitative agreement with experimental estimates for the adsorption energy of aromatic molecules thus validates the soundness of our hybrid QM/MM scheme.

Demystifying the Atomistic Origin of the Electric Field Effect on Methane Oxidation.

Understanding the role of an electric field on the surface of a catalyst is crucial in tuning and promoting the catalytic activity of metals. Herein, we evaluate the oxidation of methane over a Pt surface with varying oxygen coverage using density functional theory. The latter is controlled by the electrode polarization, giving rise to the non-Faradaic modification of catalytic activity phenomenon. At -1 V, the Pt(111) surface is present, while at 1 V, α-PtO2 on Pt(111) takes over. Our results demonstrate that the alteration of the platinum oxide surface under the influence of an electrochemical potential promotes the catalytic activity of the metal oxides by lowering the activation energy barrier of the reaction.

Water adlayers on noble metal surfaces: Insights from energy decomposition analysis.

Water molecules adsorbed on noble metal surfaces are of fundamental interest in surface science, in heterogeneous catalysis, and as a model for the metal/water interface. Herein, we analyze 28 water structures adsorbed on five noble metal surfaces (Cu, Ag, Au, Pd, and Pt) via density functional theory and energy decomposition analysis based on the block localized wave function technique. Structures, ranging from monomers to ice adlayers, reveal that the charge transfer from water to the surface is nearly independent from the charge transfer between the water molecules, while the polarization energies are cooperative. Dense water-water networks with small surface dipoles, such as the 39×39 unit cell [experimentally observed on Pt(111)], are favored compared to the highly ordered and popular Hup and Hdown phases. The second main result of our study is that the many-body interactions, which stabilize the water assemblies on the metal surfaces, are dominated by the polarization energies, with the charge transfer scaling with the polarization energies. Hence, if an empirical model could be found that reproduces the polarization energies, the charge transfer could be predicted as well, opening exciting perspectives for force field development.

Revisiting the Active Sites at the MoS2/H2O Interface via Grand-Canonical DFT: The Role of Water Dissociation.

MoS2 is a promising low-cost catalyst for the hydrogen evolution reaction (HER). However, the nature of the active sites remains a subject of debate. By taking the electrochemcal potential explicitly into account using grand-canonical density functional theory (DFT) in combination with the linearized Poisson-Boltzmann equation, we herein revisit the active sites of 2H-MoS2. In addition to the well-known catalytically active edge sites, also specific point defects on the otherwise inert basal plane provide highly active sites for HER. Given that HER takes place in water, we also assess the reactivity of these active sites with respect to H2O. The thermodynamics of proton reduction as a function of the electrochemical potential reveals that four edge sites and three basal plane defects feature thermodynamic overpotentials below 0.2 V. In contrast to current proposals, many of these active sites involve adsorbed OH. The results demonstrate that even though H2O and OH block "active" sites, HER can also occur on these "blocked" sites, reducing protons on surface OH/H2O entities. As a consequence, our results revise the active sites, highlighting the so far overlooked need to take the liquid component (H2O) of the functional interface into account when considering the stability and activity of the various active sites.