Anti-quorum sensing activity of α-amidoamides against Agrobacterium tumefaciensNT1: Insights from molecular docking and dynamic investigations to synergistic approach of metronidazole release from gel formulations

A unique approach is imperative for the development of drugs aimed at inhibiting various stages of infection, rather than solely focusing on bacterial viability. Among the array of unconventional targets explored for formulating novel antimicrobial medications, blocking the quorum-sensing (QS) system emerges as a highly effective and promising strategy against a variety of pathogenic microbes. In this investigation, we have successfully assessed nine α-aminoamides for their anti-QS activity using Agrobacterium tumefaciensNT1 as a biosensor strain. Among these compounds, three (2, 3and, 4) have been identified as potential anti-QS candidates. Molecular docking studies have further reinforced these findings, indicating that these compounds exhibit favorable pharmacokinetic profiles. Additionally, we have assessed the ligand's stability within the protein's binding pocket using molecular dynamics (MD) simulations and MMGBSA analysis. Further, combination of antiquorum sensing properties with antibiotics viaself-assembly represents a promising approach to enhance antibacterial efficacy, overcome resistance, and mitigate the virulence of bacterial pathogens. The release study also reflects a slow and gradual release of the metronidazole at both pH 6.5 and pH 7.4, avoiding the peaks and troughs associated with more immediate release formulations.

Stable Pentagonal Layered Palladium Diselenide Enables Rapid Electrosynthesis of Hydrogen Peroxide

Electrosynthesis of hydrogen peroxide (H2O2) via the two-electron oxygen reduction reaction (2e- ORR) is promising for various practical applications, such as wastewater treatment. However, few electrocatalysts are active and selective for 2e- ORR yet are also resistant to catalyst leaching under realistic operating conditions. Here, a joint experimental and computational study reveals active and stable 2e- ORR catalysis in neutral media over layered PdSe2 with a unique pentagonal puckered ring structure type. Computations predict active and selective 2e- ORR on the basal plane and edge of PdSe2, but with distinct kinetic behaviors. Electrochemical measurements of hydrothermally synthesized PdSe2 nanoplates show a higher 2e- ORR activity than other Pd-Se compounds (Pd4Se and Pd17Se15). PdSe2 on a gas diffusion electrode can rapidly accumulate H2O2 in buffered neutral solution under a high current density. The electrochemical stability of PdSe2 is further confirmed by long device operational stability, elemental analysis of the catalyst and electrolyte, and synchrotron X-ray absorption spectroscopy. This work establishes a new efficient and stable 2e- ORR catalyst at practical current densities and opens catalyst designs utilizing the unique layered pentagonal structure motif.

Adsorption of per- and poly-fluoroalkyl substances (PFAS) on Ni: A DFT investigation

Electrocatalytic destruction of per- and polyfluoroalkyl substances (PFAS) is an emerging approach for treatment of PFAS-contaminated water. In this study, a systematic ab initio investigation of PFAS adsorption on Ni, a widely used electrocatalyst, was conducted by means of dispersion-corrected Density Functional Theory (DFT) calculations. The objective of this investigation was to elucidate the adsorption characteristics and charge transfer mechanisms of different PFAS molecules on Ni surfaces. PFAS adsorption on three of the most thermodynamically favorable Ni surface facets, namely (001), (110), and (111), was investigated. Additionally, the role of PFAS chain length and functional group was studied by comparing the adsorption characteristics of different PFAS compounds, namely perfluorooctanesulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorobutanesulfonic acid (PFBS), and perfluorobutanoic acid (PFBA). For each PFAS molecule-Ni surface facet pair, different adsorption configurations were considered. Further calculations were carried out to reveal the effect of solvation, pre-adsorbed atomic hydrogen (H), and surface defects on the adsorption energy. Overall, the results revealed that the adsorption of PFAS on Ni surfaces is energetically favorable, and that the adsorption is primarily driven by the functional groups. The presence of preadsorbed H and the inclusion of solvation produced less exothermic adsorption energies, while surface vacancy defects showed mixed effects on PFAS adsorption. Taken together, the results of this study suggest that Ni is a promising electrocatalyst for PFAS adsorption and destruction, and that proper control for the exposed facets and surface defects could enhance the adsorption stability.

Transferable Water Potentials Using Equivariant Neural Networks

Machine learning interatomic potentials (MLIPs) have emerged as a technique that promises quantum theory accuracy for reduced cost. It has been proposed [J. Chem. Phys. 2023, 158, 084111] that MLIPs trained on solely liquid water data cannot accurately transfer to the vapor-liquid equilibrium while recovering the many-body decomposition (MBD) analysis of gas-phase water clusters. This suggests that MLIPs do not directly learn the physically correct interactions of water molecules, limiting transferability. In this work, we show that MLIPs using equivariant architecture and trained on 3200 liquid water structures reproduces liquid-phase water properties (e.g., density within 0.003 g/cm3 between 230 and 365 K), vapor-liquid equilibrium properties up to 550 K, the MBD analysis of gas-phase water cluster up to six-body interactions, and the relative energy and the vibrational density of states of ice phases. We show that potentials developed using equivariant MLIPs allow transferability for arbitrary phases of water that remain stable in nanosecond long simulations.

Cavity formation at metal-water interfaces

The free energy cost of forming a cavity in a solvent is a fundamental concept in rationalizing the solvation of molecules and ions. A detailed understanding of the factors governing cavity formation in bulk solutions has inter alia enabled the formulation of models that account for this contribution in coarse-grained implicit solvation methods. Here, we employ classical molecular dynamics simulations and multistate Bennett acceptance ratio free energy sampling to systematically study cavity formation at a wide range of metal-water interfaces. We demonstrate that the obtained size- and position-dependence of cavitation energies can be fully rationalized by a geometric Gibbs model, which considers that the creation of the metal-cavity interface necessarily involves the removal of interfacial solvent. This so-called competitive adsorption effect introduces a substrate dependence to the interfacial cavity formation energy that is missed in existing bulk cavitation models. Using expressions from scaled particle theory, this substrate dependence is quantitatively reproduced by the Gibbs model through simple linear relations with the adsorption energy of a single water molecule. Besides providing a better general understanding of interfacial solvation, this paves the way for the derivation and efficient parametrization of more accurate interface-aware implicit solvation models needed for reliable high-throughput calculations toward improved electrocatalysts.

Stay Hydrated! Impact of Solvation Phenomena on the CO2 Reduction Reaction at Pb(100) and Ag(100) surfaces

Herein, a comprehensive computational study of the impact of solvation on the reduction reaction of CO2 to formic acid (HCOOH) and carbon monoxide on Pb(100) and Ag(100) surfaces is presented. Results further the understanding of how solvation phenomena influence the adsorption energies of reaction intermediates. We applied an explicit solvation scheme harnessing a combined density functional theory (DFT)/microkinetic modeling approach for the CO2 reduction reaction. This approach reveals high selectivities for CO formation at Ag and HCOOH formation on Pb, resolving the prior disparity between ab initio calculations and experimental observations. Furthermore, the detailed analysis of adsorption energies of relevant reaction intermediates shows that the total number of hydrogen bonds formed by HCOO plays a primary role for the adsorption strength of intermediates and the electrocatalytic activity. Results emphasize the importance of explicit solvation for adsorption and electrochemical reaction phenomena on metal surfaces.

Exploring the biointerfaces: ab initio investigation of nano-montmorillonite clay, and its interaction with unnatural amino acids

We investigated the interaction between biomimetic Fe and Mg co-doped montmorillonite nanoclay and eleven unnatural amino acids. Employing three different functionals (PBE-GGA, PBE-GGA + U, and HSE06), we examined the clay's structural, electronic, and magnetic properties. Our results revealed the necessity of using PBE-GGA + U with U ≥ 4 eV to accurately describe key clay properties. We identified amino acids that strongly interacted with the clay surface, with steric orientation playing a crucial role in facilitating binding. Our DFT calculations highlighted significant electrostatic interactions between the amino acids and the clay slab, with the amino group's predominant role in this interaction. These findings hold promise for designing amino acids for clay-amino acid systems, leading to innovative bio-material composites for various applications. Additionally, our ab-initio molecular dynamics simulations confirmed the stability of clay-amino acid systems under ambient conditions, and the introduction of an implicit water solvent enhanced the binding energy of amino acids on the clay surface.

Recent advancement of HDAC inhibitors against breast cancer

Recent studies highlight the great potential impact of HDAC inhibitors (HDACis) in suppressing TNBC, even though clinical trials including a single HDACis demonstrated unsatisfactory outcomes against TNBC. New compounds created to achieve isoform selectivity and/or a polypharmacological HDAC strategy have also produced interesting results. The current study discusses the HDACis pharmacophoric models and the structural alterations that produced drugs with strong inhibitory effects on TNBC progression. With more than 2 million new cases reported in 2018, breast cancer-the most common cancer among women worldwide-poses a significant financial burden on an already deteriorating public health system. Due to a lack of therapies being developed for triple-negative breast cancers and the development of resistance to the current treatment options, it is imperative to plan novel therapeutics in order to bring new medications to the pipeline. Additionally, HDACs deacetylate a large number of nonhistone cellular substrates that control a variety of biological processes, such as the beginning and development of cancer. The significance of HDACs in cancer and the therapeutic potential of HDAC inhibitor. Furthermore, we also reported molecular docking study with four HDAC inhibitors and performed molecular dynamic stimulation of the best dock score compound. Among the four ligands belinostat compound showed best binding affinity with histone deacetylase protein which was -8.7 kJ/mol. It also formed five conventional hydrogen bond with Gly 841, His 669, His 670, pro 809, and His 709 amino acid residues.

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.

The application of QM/MM simulations in heterogeneous catalysis

The QM/MM simulation method is provenly efficient for the simulation of biological systems, where an interplay of extensive environment and delicate local interactions drives a process of interest through a funnel on a complex energy landscape. Recent advances in quantum chemistry and force-field methods present opportunities for the adoption of QM/MM to simulate heterogeneous catalytic processes, and their related systems, where similar intricacies exist on the energy landscape. Herein, the fundamental theoretical considerations for performing QM/MM simulations, and the practical considerations for setting up QM/MM simulations of catalytic systems, are introduced; then, areas of heterogeneous catalysis are explored where QM/MM methods have been most fruitfully applied. The discussion includes simulations performed for adsorption processes in solvent at metallic interfaces, reaction mechanisms within zeolitic systems, nanoparticles, and defect chemistry within ionic solids. We conclude with a perspective on the current state of the field and areas where future opportunities for development and application exist.

Differences in solvation thermodynamics of oxygenates at Pt/Al2O3 perimeter versus Pt(111) terrace sites

A prominent role of water in aqueous-phase heterogeneous catalysis is to modify free energies; however, intuition about how is based largely on pure metal surfaces or even homogeneous solutions. Using multiscale modeling with explicit liquid water molecules, we show that the influence of water on the free energies of adsorbates at metal/support interfaces is different than that on pure metal surfaces. We specifically compute free energies of solvation for methanol and its constituents on a Pt/Al₂O₃ catalyst and compare the results to analogous values calculated on a pure Pt catalyst. We find that the more hydrophilic Pt/Al₂O₃ interface leads to smaller (more positive) free energies of solvation due to an increased entropy penalty resulting from the additional work necessary to disrupt the interfacial water structure and accommodate the interfacial species. The results will be of interest in other fields, including adsorption and proteins.

Ab initio calculation of the adsorption of As, Cd, Cr, and Hg heavy metal atoms onto the illite(001) surface: Implications for soil pollution and reclamation

Elucidating the mechanisms of heavy metal (HM) adsorption on clay minerals is key to solving HM pollution in soil. In this study, the adsorption of four HM atoms (As, Cd, Cr, and Hg) on the illite(001) surface was investigated using density functional theory calculations. Different adsorption configurations were investigated and the electronic properties (i.e., adsorption energy (E_ad) and electron transfer) were analyzed. The E_ad values of the four HM atoms on the illite(001) surface were found to be As > Cr > Cd > Hg. The E_ad values for the most stable adsorption configurations of As, Cr, Cd, and Hg were -1.8554, -0.7982, -0.3358, and -0.2678 eV, respectively. The As atoms show effective chemisorption at all six adsorption sites, while Cd, Cr, and Hg atoms mainly exhibited physisorption. The hollow and top (O) sites were more favorable than the top (K) sites for the adsorption of HM atoms. The Gibbs free energy results show that the illite(001) surface was energetically favorable for the adsorption of As and Cr atoms under the influence of 298 K and 1 atm. After adsorption, there was a redistribution of positions and reconfiguration of the chemical bonding of the surface atoms, with a non-negligible influence around the upper surface atoms. Bader charge analysis shows electrons were transferred from the surface to the HM atoms, and a strong correlation between the valence electron variations and the adsorption energy was observed. HM atoms had a high electronic state overlap with the surface O atoms near the Fermi energy level, indicating that the surface O atoms, though not the topmost atoms around the surface, significantly influence HM adsorption. The above results show illite(001) preferentially adsorbed As among all four investigated HM atoms, indicating that soils containing a high proportion of illite might be more prone to As pollution.

Liquid-Phase Effects on Adsorption Processes in Heterogeneous Catalysis

Aqueous solvation free energies of adsorption have recently been measured for phenol adsorption on Pt(111). Endergonic solvent effects of ∼1 eV suggest solvents dramatically influence a metal catalyst's activity with significant implications for the catalyst design. However, measurements are indirect and involve adsorption isotherm models, which potentially reduces the reliability of the extracted energy values. Computational, implicit solvation models predict exergonic solvation effects for phenol adsorption, failing to agree with measurements even qualitatively. In this study, an explicit, hybrid quantum mechanical/molecular mechanical approach for computing solvation free energies of adsorption is developed, solvation free energies of phenol adsorption are computed, and experimental data for solvation free energies of phenol adsorption are reanalyzed using multiple adsorption isotherm models. Explicit solvation calculations predict an endergonic solvation free energy for phenol adsorption that agrees well with measurements to within the experimental and force field uncertainties. Computed adsorption free energies of solvation of carbon monoxide, ethylene glycol, benzene, and phenol over the (111) facet of Pt and Cu suggest that liquid water destabilizes all adsorbed species, with the largest impact on the largest adsorbates.

Multilevel Computational Studies Reveal the Importance of Axial Ligand for Oxygen Reduction Reaction on Fe-N-C Materials

The systematic improvement of Fe-N-C materials for fuel cell applications has proven challenging, due in part to an incomplete atomistic understanding of the oxygen reduction reaction (ORR) under electrochemical conditions. Herein, a multilevel computational approach, which combines ab initio molecular dynamics simulations and constant potential density functional theory calculations, is used to assess proton-coupled electron transfer (PCET) processes and adsorption thermodynamics of key ORR intermediates. These calculations indicate that the potential-limiting step for ORR on Fe-N-C materials is the formation of the Fe^III-OOH intermediate. They also show that an active site model with a water molecule axially ligated to the iron center throughout the catalytic cycle produces results that are consistent with the experimental measurements. In particular, reliable prediction of the ORR onset potential and the Fe(III/II) redox potential associated with the conversion of Fe^III-OH to Fe^II and desorbed H₂O requires an axial H₂O co-adsorbed to the iron center. The observation of a five-coordinate rather than four-coordinate active site has significant implications for the thermodynamics and mechanism of ORR. These findings highlight the importance of solvent-substrate interactions and surface charge effects for understanding the PCET reaction mechanisms and transition-metal redox couples under realistic electrochemical conditions.

Challenges of modeling nanostructured materials for photocatalytic water splitting

Understanding the water splitting mechanism in photocatalysis is a rewarding goal as it will allow producing clean fuel for a sustainable life in the future. However, identifying the photocatalytic mechanisms by modeling photoactive nanoparticles requires sophisticated computational techniques based on multiscale modeling. In this review, we will survey the strengths and drawbacks of currently available theoretical methods at different length and accuracy scales. Understanding the surface-active site through Density Functional Theory (DFT) using new, more accurate exchange-correlation functionals plays a key role for surface engineering. Larger scale dynamics of the catalyst/electrolyte interface can be treated with Molecular Dynamics albeit there is a need for more generalizations of force fields. Monte Carlo and Continuum Modeling techniques are so far not the prominent path for modeling water splitting but interest is growing due to the lower computational cost and the feasibility to compare the modeling outcome directly to experimental data. The future challenges in modeling complex nano-photocatalysts involve combining different methods in a hierarchical way so that resources are spent wisely at each length scale, as well as accounting for excited states chemistry that is important for photocatalysis, a path that will bring devices closer to the theoretical limit of photocatalytic efficiency.

Theoretical investigation of the cooperative effect of solvent: a case study

The effect of solvent was investigated at the DFT level, M06-2X/6-31++G(d,p), for the implicit, namely the universal solvent model based on solute electron density (SMD), and hybrid solvation models, and...

Implicit Solvation Methods for Catalysis at Electrified Interfaces

Implicit solvation is an effective, highly coarse-grained approach in atomic-scale simulations to account for a surrounding liquid electrolyte on the level of a continuous polarizable medium. Originating in molecular chemistry with finite solutes, implicit solvation techniques are now increasingly used in the context of first-principles modeling of electrochemistry and electrocatalysis at extended (often metallic) electrodes. The prevalent ansatz to model the latter electrodes and the reactive surface chemistry at them through slabs in periodic boundary condition supercells brings its specific challenges. Foremost this concerns the difficulty of describing the entire double layer forming at the electrified solid–liquid interface (SLI) within supercell sizes tractable by commonly employed density functional theory (DFT). We review liquid solvation methodology from this specific application angle, highlighting in particular its use in the widespread ab initio thermodynamics approach to surface catalysis. Notably, implicit solvation can be employed to mimic a polarization of the electrode’s electronic density under the applied potential and the concomitant capacitive charging of the entire double layer beyond the limitations of the employed DFT supercell. Most critical for continuing advances of this effective methodology for the SLI context is the lack of pertinent (experimental or high-level theoretical) reference data needed for parametrization.

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.

A simple method to calculate solution-phase free energies of charged species in computational electrocatalysis

Determining the adsorption potential of adsorbed ions in the field of computational electrocatalysis is of great interest to study their interaction with the electrode material and the solvent, and to map out surface phase diagrams and reaction pathways. Calculating the adsorption potentials of ions with density functional theory and comparing across various ions requires an accurate reference energy of the ion in solution and electrons at the same electrochemical scale. Here we highlight a previously used method for determining the reference free energy of solution phase ions using a simple electrochemical thermodynamic cycle, which allows this free energy to be calculated from that of a neutral gas-phase or solid species and an experimentally measured equilibrium potential, avoiding the need to model solvent around the solution phase ion in the electronic structure calculations. While this method is not new, we describe its use and utility in detail and show that this same method can be used to find the free energy of any ion from any reaction, as long as the half-cell equilibrium potential is known, even for reactions that do not transfer the same number of protons and electrons. To illustrate its usability, we compare the adsorption potentials obtained with DFT of I^*, Br^*, Cl^*, and SO₄^*on Pt(111) and Au(111) and OH^*and Ag^*on Pt(111) with those measured experimentally and find that this simple and computationally affordable method reproduces the experimental trends.

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.

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.

Ten Facets, One Force Field: The GAL19 Force Field for Water-Noble Metal Interfaces

Understanding the structure of the water/metal interfaces plays an important role in many areas ranging from surface chemistry to environmental processes. The size, required phase-space sampling, and the slow diffusion of molecules at the water/metal interfaces motivate the development of accurate force fields. We develop and parametrize GAL19, a novel force field, to describe the interaction of water with two facets (111 and 100) of five metals (Pt, Pd, Au, Ag, Cu). To increase transferability compared to its predecessor GAL17, the water-metal interaction is described as a sum of pairwise terms. The interaction energy has three contributions: (i) physisorption is described via a Tang and Toennies potential, (ii) chemisorption and surface corrugation rely on an attractive Gaussian term, and (iii) the angular dependence is explicitly included as a truncated Fourier series. Thirteen parameters are used for each metal surface and were fitted on 250 water adsorption energies computed at the PBE+dDsC level. The performance of GAL19 was evaluated on a set of more than 600 DFT adsorption energies for each surface, leading to an average root-mean-square deviation of only 1 kcal/mol, correctly reproducing the adsorption trends: strong on Pt and Pd but weaker on Ag, Au, and Cu. This force field was then used to simulate the water/metal interface for all ten surfaces for 1 ns. Structural analyses reveal similar tendencies for all surfaces: a first, dense water layer that is mostly adsorbed on the metal top sites and a second layer up to around 6 Å, which is less structured. On Pt and Pd, the first layer is strongly organized with water lying flat on the surface. The pairwise additive functional form allows one to simulate the water adsorption on alloys, which is demonstrated at the example of Ag/Cu and Au/Pt alloys. The water/Ag-Cu interface is predicted to be disordered with water mostly adsorbed on Cu which should exacerbate the Ag reactivity. On the contrary, incorporating Pt into Au materials leads to a structuring of the water interface. Our promising results make GAL19 an ideal candidate to get representative sampling of complex metal/water interfaces as a first step toward accurate estimation of free energies of reactions in solution at the metal interface.

Parameter-free coordination numbers for solutions and interfaces

Coordination numbers are among the central quantities to describe the local environment of atoms and are thus used in various applications such as structure analysis, fingerprints, and parameters. Yet, there is no consensus regarding a practical algorithm, and many proposed methods are designed for specific systems. In this work, we propose a scale-free and parameter-free algorithm for nearest neighbor identification. This algorithm extends the powerful Solid-Angle based Nearest-Neighbor (SANN) framework to explicitly include local anisotropy. As such, our Anisotropically corrected SANN (ASANN) algorithm provides with a fast, robust, and adaptive method for computing coordination numbers. The ASANN algorithm is applied to flat and corrugated metallic surfaces to demonstrate that the expected coordination numbers are retrieved without the need for any system-specific adjustments. The same applies to the description of the coordination numbers of metal atoms in AuCu nanoparticles, and we show that ASANN based coordination numbers are well adapted for automatically counting neighbors and the establishment of cluster expansions. Analysis of classical molecular dynamics simulations of an electrified graphite electrode reveals a strong link between the coordination number of Cs⁺ ions and their position within the double layer, a relation that is absent for Na⁺, which keeps its first solvation shell even close to the electrode.

Practical Considerations for Continuum Models Applied to Surface Electrochemistry

Modelling the electrolyte at the electrochemical interface remains a major challenge in ab initio simulations of charge transfer processes at surfaces. Recently, the development of hybrid polarizable continuum models/ab initio models have allowed for the treatment of solvation and electrolyte charge in a computationally efficient way. However, challenges remain in its application. Recent literature has reported that large cell heights are required to reach convergence, which presents a serious computational cost. Furthermore, calculations of reaction energetics require costly iterations to tune the surface charge to the desired potential. In this work, we present a simple capacitor model of the interface that illuminates how to circumvent both of these challenges. We derive a correction to the energy for finite cell heights to obtain the large cell energies at no additional computational expense. We furthermore demonstrate that the reaction energetics determined at constant charge are easily mapped to those at constant potential, which eliminates the need to apply iterative schemes to tune the system to a constant potential. These developments together represent more than an order of magnitude reduction of the computational overhead required for the application of polarizable continuum models to surface electrochemistry.

Theoretical insight into the origin of the electrochemical promotion of ethylene oxidation on ruthenium oxide

In EPOC the adsorption energies of the reactants and products are modified by applying an electrochemical potential to the catalyst. DFT computations unveil that the C–C and O–O bond dissociation are accelerated under positive and negative potential, respectively.

Can microsolvation effects be estimated from vacuum computations? A case-study of alcohol decomposition at the H2O/Pt(111) interface

Activation and reaction energies of alcohol decomposition at Pt(111) are barely modified by a PCM, in contrast to adding a single water molecule, whose effect can be predicted based on vacuum computations.

Force Field for Water over Pt(111): Development, Assessment, and Comparison

Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H₂O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H₂O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.

Origin of the overpotentials for HCOO− and CO formation in the electroreduction of CO2 on Cu(211): the reductive desorption processes decide

Potential-related free energy profiles of CO and HCOO⁻ pathways in CO₂RR on Cu(211) are computed with implicit solvent model.