Comprehensive Benchmarking of a Density-Dependent Dispersion Correction

On the nature of Cu-carbon interaction through N-modification for enhanced ethanol synthesis from syngas and methanol

Direct conversion of syngas into ethanol is an attractive process because of its short route and high-added value, but remains an enormous challenge due to the low selectivity caused by unclear active sites. Here, the Cu(111) supported N-modified graphene fragments C13-mNm/Cu(111) (m = 0-2) are demonstrated to be an efficient catalyst for fabricating ethanol from syngas and methanol. Our results suggest that the Cu-carbon interaction not only facilitates CO activation, but also significantly affects the adsorption stability of C2 intermediates and finally changes the fundamental reaction mechanism. The impeded hydrogenation performance of C13/Cu(111) due to the introduced Cu-carbon interaction is dramatically improved by N-doping. Multiple analyses reveal that the promoted electron transfer and the enhanced electron endowing ability of C13-mNm/Cu(111) (m = 1-2) to the co-adsorbed CH3CHxOH (x = 0-1) and H are deemed to be mainly responsible for the remarkable enhancement in hydrogenation ability. From the standpoint of the frontier molecular orbital, the decreased HOMO-LUMO gap and the increased overlap extent of HOMO and LUMO with the doping of N atoms also further verify the more facile hydrogenation reactions. Clearly, the Cu-carbon interaction through N-modification is of critical importance in ethanol formation. The final hydrogenation reaction during ethanol formation is deemed to be the rate-controlling step. The insights gained here could shed new light on the nature of Cu-carbon interaction in carbon material modified Cu-based catalysts for ethanol synthesis, which could be extended to design and modify other metal-carbon catalysts.

Microkinetic Molecular Volcano Plots for Enhanced Catalyst Selectivity and Activity Predictions

Molecular volcano plots, which facilitate the rapid prediction of the activity and selectivity of prospective catalysts, have emerged as powerful tools for computational catalysis. Here, we integrate microkinetic modeling into the volcano plot framework to develop "microkinetic molecular volcano plots". The resulting unified computational framework allows the influence of important reaction parameters, including temperature, reaction time, and concentration, to be quickly incorporated and more complex situations, such as off-cycle resting states and coupled catalytic cycles, to be tackled. Compared to previous generations of molecular volcanoes, these microkinetic counterparts offer a more comprehensive understanding of catalytic behavior, in which selectivity and product ratios can be explicitly determined by tracking the evolution of each product concentration over time. This is demonstrated by examining two case studies, rhodium-catalyzed hydroformylation and metal-catalyzed hydrosilylation, in which the unique insights provided by microkinetic modeling, as well as the ability to simultaneously screen catalysts and reaction conditions, are highlighted. To facilitate the construction of these plots/maps, we introduce mikimo, a Python program that seamlessly integrates with our previously developed automated volcano builder, volcanic.

Managing Expectations and Imbalanced Training Data in Reactive Force Field Development: An Application to Water Adsorption on Alumina

ReaxFF is a computationally efficient model for reactive molecular dynamics simulations that has been applied to a wide variety of chemical systems. When ReaxFF parameters are not yet available for a chemistry of interest, they must be (re)optimized, for which one defines a set of training data that the new ReaxFF parameters should reproduce. ReaxFF training sets typically contain diverse properties with different units, some of which are more abundant (by orders of magnitude) than others. To find the best parameters, one conventionally minimizes a weighted sum of squared errors over all of the data in the training set. One of the challenges in such numerical optimizations is to assign weights so that the optimized parameters represent a good compromise among all the requirements defined in the training set. This work introduces a new loss function, called Balanced Loss, and a workflow that replaces weight assignment with a more manageable procedure. The training data are divided into categories with corresponding "tolerances", i.e., acceptable root-mean-square errors for the categories, which define the expectations for the optimized ReaxFF parameters. Through the Log-Sum-Exp form of Balanced Loss, the parameter optimization is also a validation of one's expectations, providing meaningful feedback that can be used to reconfigure the tolerances if needed. The new methodology is demonstrated with a nontrivial parametrization of ReaxFF for water adsorption on alumina. This results in a new force field that reproduces both the rare and frequent properties of a validation set not used for training. We also demonstrate the robustness of the new force field with a molecular dynamics simulation of water desorption from a γ-Al2O3 slab model.

Hybrid RPA:DFT Approach for Adsorption on Transition Metal Surfaces: Methane and Ethane on Platinum (111)

The hybrid QM:QM approach is extended to adsorption on transition metal surfaces. The random phase approximation (RPA) as the high-level method is applied to cluster models and, using the subtractive scheme, embedded in periodic models which are treated with density functional theory (DFT) that is the low-level method. The PBE functional, both without dispersion and augmented with the many-body dispersion (MBD), is employed. Adsorption of methane and ethane on the Pt(111) surface is studied. For methane in a 2 × 2 surface cell, the hybrid RPA:PBE and RPA:PBE+MBD results, -14.3 and -16.0 kJ mol-1, respectively, are in close agreement with the periodic RPA value of -13.8 kJ mol-1 at significantly reduced computational cost (factor of ∼50). For methane and ethane, the RPA:PBE results (-14.3 and -17.8 kJ mol-1, respectively) indicate underbinding relative to energies derived from experimental desorption barriers for relevant loadings (-15.6 ± 1.6 and -27.2 ± 2.9 kJ mol-1, respectively), whereas the hybrid RPA:PBE+MBD results (-16.0 and -24.9 kJ mol-1, respectively) agree with the experiment well within experimental uncertainty limits (deviation of -0.4 ± 1.5 and +2.3 ± 2.9 kJ mol-1, respectively). Finding a cluster that adequately and robustly represents the adsorbate at the bulk surface is important for the success of the RPA-based QM:QM scheme for metals.

Decoding Van der Waals Impact on Chirality Transfer in Perovskite Structures: Density Functional Theory Insights

Chiral organic-inorganic perovskites exhibit unique physicochemical properties driven by the symmetry of monovalent organic cations. However, an atomistic understanding of how chiral cations transfer their chirality to the inorganic framework and the role played by van der Waals (vdW) interactions in this process is still incomplete. In this work, we report a theoretical investigation, based on density functional theory calculations within the Perdew-Burke-Ernzerhof (PBE) formulation for the exchange-correlation functional, into the role of the vdW interactions in the chirality transfer process. For that, we selected several vdW corrections, namely, Grimme (D2, D3, D3(BJ)), Tkatchenko-Scheffler (TS, TS+SCS, TS+HSI), density-dependent energy correction (dDsC), and many-body scattering (MBD) energy method correction. For the chiral perovskite systems, we selected a set of chiral organic-inorganic perovskites with several dimensions, namely, from zero-dimensional to three-dimensional, each having enantiomers with R and S configurations. Based on a statistical treatment of the relative errors of all lattice parameters with respect to experimental data, we found that D3, D3(BJ), TS, TS+SCS, TS+HSI, and MBD vdW are the most accurate corrections to describe the equilibrium structural properties of chiral perovskites using the PBE method. We identify chirality-induced sequential asymmetries of distorted octahedrons and propose angular descriptors to quantify them, where the orientations of these distortions depend on the R or S nature of the chiral cations. Furthermore, we demonstrate the importance of accurate vdW interactions in precisely describing these asymmetric distortions. By means of binding energies and charge-transfer analysis, we show that the impact of vdW corrections on the charge distribution leads to a subtle strengthening of hydrogen bonds between chiral cations and inorganic octahedra, resulting in an increase in the binding energy. Finally, we identified that the Rashba-Dresselhaus effect in two-dimensionality is refined by vdW interactions.

Tuning the Hydrogenation Selectivity of an Unsaturated Aldehyde via Single-Atom Alloy Catalysts

Selective hydrogenation of α,β-unsaturated aldehydes to produce unsaturated alcohols remains a challenge in catalysis. Here, we explore, on the basis of first-principles simulations, single-atom alloy (SAA) catalysts on copper as a class of catalytic materials to enhance the selectivity for C═O bond hydrogenation in unsaturated aldehydes by controlling the binding strength of the C═C and C═O bonds. We show that on SAA of early transition metals such as Ti, Zr, and Hf, the C═O binding mode of acrolein is favored but the strong binding renders subsequent hydrogenation and desorption impossible. On SAA of late-transition metals, on the other hand, the C═C binding mode is favored and C═C bond hydrogenation follows, resulting in the production of undesired saturated aldehydes. Mid-transition metals (Cr and Mn) in Cu(111) appear as the optimal systems, since they favor acrolein adsorption via the C═O bond but with a moderate binding strength, compatible with catalysis. Additionally, acrolein migration from the C═O to the C═C binding mode, which would open the low energy path for C═C bond hydrogenation, is prevented by a large barrier for this process. SAA of Cr in Cu appears as an optimal candidate, and kinetic simulations show that the selectivity for propenol formation is controlled by preventing the acrolein migration from the more stable C═O to the less stable C═C binding mode and subsequent H-migration and by the formation of the O-H bond from the monohydrogenated intermediate. Dilute alloy catalysts therefore enable tuning the binding strength of intermediates and transition states, opening control of catalytic activity and selectivity.

Tracking of the conversion and transformation pathways of dissolved organic matter in sludge hydrothermal liquids during Cr(VI) reduction using FT-ICR MS

In this study, the remediation effects of two types of sludge (ferric-based flocculant and non-ferric-based flocculant) on Cr(VI)-polluted wastewater were evaluated to clarify the key components in sludge hydrothermal solutions responsible for reducing Cr(VI) and understand the underlying molecular-level transformation mechanisms. The results revealed that the primary reactions during the hydrothermal processes were deamination and decarboxylation reactions. Correlation analysis highlighted proteins, reducing sugars, amino groups, and phenolic hydroxyl groups as the major contributors. In-depth analysis of the transformation process of functional groups within dissolved organic matter (DOM) and synergistic redox process between Cr(VI) and DOM in hydrothermal solutions demonstrated that phenolic hydroxyl and amino groups gradually underwent oxidation during reduction of Cr(VI) by DOM, forming aldehyde and carboxyl groups, among the others. Time-dependent density functional theory calculations revealed notable shift of reducing functional groups from ground state to excited state following iron complexation, ultimately facilitating reduction reaction. Subsequent investigations, including soil column leaching and seed germination rate tests, indicated that synergistic redox interaction between Cr(VI) and DOM significantly reduced waterborne heavy metal and toxic organic pollution. These findings carry substantial implications for sludge treatment and remediation of heavy metal pollution in wastewater, offering valuable insights into effective environmental remediation strategies.

Toward accurate modeling of structure and energetics of bulk hexagonal boron nitride

Materials that exhibit both strong covalent and weak van der Waals interactions pose a considerable challenge to many computational methods, such as DFT. This makes assessing the accuracy of calculated properties, such as exfoliation energies in layered materials like hexagonal boron nitride (h-BN) problematic, when experimental data are not available. In this paper, we investigate the accuracy of equilibrium lattice constants and exfoliation energy calculation for various DFT-based computational approaches in bulk h-BN. We contrast these results with available experiments and reference fixed-node diffusion quantum Monte Carlo (QMC) results. From our reference QMC calculation, we obtained an exfoliation energy of - 33 ± 2 meV/atom (-0.38 ± 0.02 J/m2 ).

Revealing the Nature of Active Oxygen Species and Reaction Mechanism of Ethylene Epoxidation by Supported Ag/α-Al2O3 Catalysts

The oxygen species on Ag catalysts and reaction mechanisms for ethylene epoxidation and ethylene combustion continue to be debated in the literature despite decades of investigation. Fundamental details of ethylene oxidation by supported Ag/α-Al2O3 catalysts were revealed with the application of high-angle annular dark-field-scanning transmission electron microscopy-energy-dispersive X-ray spectroscopy (HAADF-STEM-EDS), in situ techniques (Raman, UV-vis, X-ray diffraction (XRD), HS-LEIS), chemical probes (C2H4-TPSR and C2H4 + O2-TPSR), and steady-state ethylene oxidation and SSITKA (16O2 → 18O2 switch) studies. The Ag nanoparticles are found to carry a considerable amount of oxygen after the reaction. Density functional theory (DFT) calculations indicate the oxidative reconstructed p(4 × 4)-O-Ag(111) surface is stable relative to metallic Ag(111) under the relevant reaction environment. Multiple configurations of reactive oxygen species are present, and their relevant concentrations depend on treatment conditions. Selective ethylene oxidation to EO proceeds with surface Ag4-O2* species (dioxygen species occupying an oxygen site on a p(4 × 4)-O-Ag(111) surface) only present after strong oxidation of Ag. These experimental findings are strongly supported by the associated DFT calculations. Ethylene epoxidation proceeds via a Langmuir-Hinshelwood mechanism, and ethylene combustion proceeds via combined Langmuir-Hinshelwood (predominant) and Mars-van Krevelen (minor) mechanisms.

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.

Molybdenum(III) Amidinate: Synthesis, Characterization, and Vapor Phase Growth of Mo-Based Materials

The synthesis, characterization, and thermogravimetric analysis of tris(N,N'-di-isopropylacetamidinate)molybdenum(III), Mo(iPr-AMD)₃, are reported. Mo(iPr-AMD)₃ is a rare example of a homoleptic mononuclear complex of molybdenum(III) and fills a longstanding gap in the literature of transition metal(III) trisamidinate complexes. Thermogravimetric analysis (TGA) reveals excellent volatilization at elevated temperatures, pointing to potential applications as a vapor phase precursor for higher temperature atomic layer deposition (ALD), or chemical vapor deposition (CVD) growth of Mo-based materials. The measured TGA temperature window was 200-314 °C for samples in the 3-20 mg range. To validate the utility of Mo(iPr-AMD)₃, we demonstrate aerosol-assisted CVD growth of MoO₃ from benzonitrile solutions of Mo(iPr-AMD)₃ at 500 °C using compressed air as the carrier gas. The resulting films are characterized by X-ray photoelectron spectroscopy, X-ray diffraction, and Raman spectroscopy. We further demonstrate the potential for ALD growth at 200 °C with a Mo(iPr-AMD)₃/Ar purge/300 W O₂ plasma/Ar purge sequence, yielding ultrathin films which retain a nitride/oxynitride component. Our results highlight the broad scope utility and potential of Mo(iPr-AMD)₃ as a stable, high-temperature precursor for both CVD and ALD processes.

Simple Approach for Reconciling Cyclic Voltammetry with Hydrogen Adsorption Energy for Hydrogen Evolution Exchange Current

Cyclic voltammetry (CV) is a standard technique to analyze the current-potential characteristics of the hydrogen evolution reaction (HER). Herein, we develop a computational quantum-scaled CV model for the HER building on the Butler-Volmer relation for a one-step, one-charge transfer process. Owing to a universal and absolute rate constant verified by fitting to experimental cyclic voltammograms of elemental metals, we show that the model quantifies the exchange current─the main analytical descriptor for HER activity─solely using the hydrogen adsorption free energy obtained from density functional theory calculations. Furthermore, the model resolves controversies over analytical studies for HER kinetics.

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.

Localized magnetic moment induced by boron adatoms chemisorbed on graphene

Inducing local spin-polarization in pristine graphene is highly desirable and recent experiment shows that boron adatom chemical attachment to graphene exhibits local high spin state. Using hybrid exchange-correlation functional, we show that boron (B) monomer chemisorbed on the bridge site of graphene is energically favorable, and indeed induces a weak local spin-polarization ∼0.56μB. The localized magnetic moment can be attributed to the charge transfer from boron atom to graphene, resulting in local spin charge dominantly surrounding to the adsorbed B and neighboring carbon (C) atoms. We also surprisingly find that boron dimer can even much more stable upright anchor the same site of graphene, giving rise to sizable spin magnetic moment 2.00μB. Although the apparent spin state remains mainly contributed by Bpand Cporbitals as the case of boron monomer, the delicate and substantial charge transfer of theintra-dimerplays a fundamental role in producing such sizable local spin-polarization. We employed various van der Waals corrections to check and confirm the validity of appeared local spin-polarization. In terms of the almost identical simulated scanning tunneling microscope between boron monomer and dimer, we might tend to support the fact that boron dimer can also be chemisorbed on graphene with much larger and stable localized spin magnetic moment.

Achieving Ultra-High Selectivity to Hydrogen Production from Formic Acid on Pd-Ag Alloys

Palladium-silver-based alloy catalysts have a great potential for CO-free hydrogen production from formic acid for fuel cell applications. However, the structural factors affecting the selectivity of formic acid decomposition are still debated. Herein, the decomposition pathways of formic acid on Pd-Ag alloys with different atomic configurations have been investigated to identify the alloy structures yielding high H₂ selectively. Several Pd_xAg_1-x surface alloys with various compositions were generated on a Pd(111) single crystal; their atomic distribution and electronic structure were determined by a combination of infrared reflection absorption spectroscopy (IRAS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). It was established that the Ag atoms with Pd neighbors are electronically altered, and the degree of alteration correlates with the number of nearest Pd. Temperature-programmed reaction spectroscopy (TPRS) and DFT demonstrated that the electronically altered Ag domains create a new reaction pathway that selectively dehydrogenates formic acid. In contrast, Pd monomers surrounded by Ag are demonstrated to have a similar reactivity compared to pristine Pd(111), yielding CO and H₂O in addition to the dehydrogenation products. However, they bind to the produced CO weaker than pristine Pd, demonstrating an enhancement in resistance to CO poisoning. This work therefore shows that surface Ag domains modified by interaction with subsurface Pd are the key active sites for selective decomposition of formic acid, while surface Pd atoms are detrimental to selectivity. Hence, the decomposition pathways can be tailored for CO-free H₂ production on Pd-Ag alloy systems.

PtOx Cly (OH)z (H2 O)n Complexes under Oxidative and Reductive Conditions: Impact of the Level of Theory on Thermodynamic Stabilities

Platinum-based catalysts with Cl^- , OH^- , O^2- and H₂ O ligands, are involved in many industrial processes. Their final chemical properties are impacted by calcination and reduction applied during the preparation and activation steps. We investigate their stability under these reactive conditions with density functional theory (DFT). We benchmark various functionals (PBE-dDsC, optPBE, B3LYP, HSE06, PBE0, TPSS, RTPSS and SCAN) against ACFDT-RPA. PBE-dDsC is well adapted, although hybrid functionals are more accurate for redox reactions. Thermodynamic phase diagrams are determined by computing the chemical potential of the species as a function of temperature and partial pressures of H₂ O, HCl, O₂ and H₂ . The stability and nature of the Pt species are highly sensitive to the activation conditions. Under O₂ , high temperatures favour PtO₂ while under H₂ , platinum is easily reduced to Pt(0). Chlorine modifies the coordination sphere of platinum during calcination by stabilizing PtCl₄ and shifts the reduction of platinum to higher temperatures under H₂ .

The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling

The halogen bond complexes CF3X⋯Y and C2F3X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the π-bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C−X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the π-ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet π→π* states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.

Electronic Structure of Re2(O2CR)4Cl2 Complexes (R = H, CMe3) and Reassignment of the Electronic Absorption Spectrum of Re2(O2CCMe3)4Cl2

Electronic structure calculations on two dinuclear rhenium(III) carboxylate complexes, Re₂(O₂CH)₄Cl₂ and Re₂(O₂CCMe₃)₄Cl₂, are presented and discussed. Allowed electronic transitions for both molecules were calculated using time-dependent density functional theory (TDDFT). The results for the pivalate dimer, Re₂(O₂CCMe₃)₄Cl₂, are compared with previously reported single-crystal polarized absorption spectra obtained by Martin and co-workers (Inorg. Chem.1984, 23, 699-701). Several revisions to the previous spectral assignments are proposed.

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.

Oxidative decomposition of dimethyl methylphosphonate on rutile TiO2(110): the role of oxygen vacancies

The decomposition of dimethyl methylphosphonate (DMMP, (CH₃O)₂P(O)(CH₃)), a simulant to the toxic nerve agent Sarin, on the rutile TiO₂(110) surface has been studied with temperature programmed desorption (TPD) and density functional theory (DFT) calculations. The reactivity of the TiO₂(110) surface for DMMP decomposition is shown to be low, with mainly molecular desorption and only a small fraction of methanol and formaldehyde decomposition products seen from TPD at around 650 K. In addition, this amount of products is similar to the number of O vacancies on the surface. DFT calculations show that O vacancies are key for P-OCH₃ bond cleavage of DMMP, lowering the barrier by 0.7 eV and enabling the reactive process to occur at around 600 K. This is explained by the closer position of DMMP with respect to the surface in the presence of O vacancies. Calculations show that the produced methoxy groups can transform into gas phase formaldehyde and methanol at the considered temperature (600 K), in agreement with experiments. O-C bond cleavage of DMMP is also a viable pathway at such a high temperature (600 K) for DMMP decomposition on r-TiO₂, even in the absence of O vacancies, but the formation of a gas phase product is energetically unfavorable. O vacancies hence are the active sites for decomposition of DMMP into gas phase products on r-TiO₂(110).

Computational investigation of van der Waals corrections in the adsorption properties of molecules on the Cu(111) surface

Here, we report a computational investigation on the role of the most common van der Waals (vdW) corrections (D2, D3, D3(BJ), TS, TS+SCS, TS+HI, and dDsC) employed in density functional theory (DFT) calculations within local and semilocal exchange-correlation functionals to improve the description of the interaction between molecular species and solid surfaces. For this, we selected several molecular model systems, namely, the adsorption of small molecules (CH₃, CH₄, CO, CO₂, H₂O, and OH) on the close-packed Cu(111) surface, which bind via chemisorption or physisorption mechanisms. As expected, we found that the addition of the vdW corrections enhances the energetic stability of the Cu bulk in the face-centered cubic structure, which contributes to increasing the magnitude of the mechanical properties (elastic constants, bulk, Young, and shear modulus). Except for the TS+SCS correction, all vdW corrections substantially increase the surface energy, while the work function changes by about 0.05 eV (largest change). However, we found substantial differences among the vdW corrections when comparing its effects on interlayer spacing relaxations. Based on bulk and surface results, we selected only the D3 and dDsC vdW corrections for the study of the adsorption properties of the selected molecules on the Cu(111) surface. Overall, the addition of these vdW corrections has a greater effect on weakly interacting systems (CH₄, CO₂, H₂O), while the chemisorption systems (CH₃, CO, OH) are less affected.

Self-Assembled Decanethiolate Monolayers on Au(001): Expanding the Family of Known Phases

We have studied decanethiolate self-assembled monolayers on the Au(001) surface. Planar and striped phases, as well as disordered regions, have formed after exposing the Au surface to a decanethiol solution. The planar phases that we observe have a hexagonal symmetry and have not been previously reported for thiols on the Au(001) surface and have lower coverage compared to that of the other known thiol planar phases such as the square α phase. The striped phases that we observe are similar to the previously reported β phase but still feature unit cells that cannot be modeled as the archetype, and the coverage is also somewhat lower. The disordered decanethiolate regions are more dynamic compared to the ordered phases, confirmed with I(t) spectroscopy. This suggests that in these regions the coverage is too low in order to form ordered decanethiolate phases. Our findings contribute to the growing family of possible decanethiol formations on the Au(001) surface, for which still less is known compared to the extensive overview present for the Au(111) surface.

Constructing and interpreting volcano plots and activity maps to navigate homogeneous catalyst landscapes

Volcano plots and activity maps are powerful tools for studying homogeneous catalysis. Once constructed, they can be used to estimate and predict the performance of a catalyst from one or more descriptor variables. The relevance and utility of these tools has been demonstrated in several areas of catalysis, with recent applications to homogeneous catalysts having been pioneered by our research group. Both volcano plots and activity maps are built from linear free energy scaling relationships that connect the value of a descriptor variable(s) with the relative energies of other catalytic cycle intermediates/transition states. These relationships must be both constructed and postprocessed appropriately to obtain the resulting plots/maps; this process requires careful execution to obtain meaningful results. In this protocol, we provide a step-by-step guide to building volcano plots and activity maps using curated reaction profile data. The reaction profile data are obtained using density functional theory computations to model the catalytic cycle. In addition, we provide volcanic, a Python code that automates the steps of the process following data acquisition. Unlike the computation of individual reaction energy profiles, our tools lead to a holistic view of homogeneous catalyst performance that can be broadly applied for both explanatory and screening purposes.

Dynamical Study of Adsorbate-Induced Restructuring Kinetics in Bimetallic Catalysts Using the PdAu(111) Model System

Dynamic restructuring of bimetallic catalysts plays a crucial role in their catalytic activity and selectivity. In particular, catalyst pretreatment with species such as carbon monoxide and oxygen has been shown to be an effective strategy for tuning the surface composition and morphology. Mechanistic and kinetic understanding of such restructuring is fundamental to the chemistry and engineering of surface active sites but has remained challenging due to the large structural, chemical, and temporal degrees of freedom. Here, we combine time-resolved temperature-programmed infrared reflection absorption spectroscopy, ab initio thermodynamics, and machine-learning molecular dynamics to uncover previously unidentified timescale and kinetic parameters of in situ restructuring in Pd/Au(111), a highly relevant model system for dilute Pd-in-Au nanoparticle catalysts. The key innovation lies in utilizing CO not only as a chemically sensitive probe of surface Pd but also as an agent that induces restructuring of the surface. Upon annealing in vacuum, as-deposited Pd islands became encapsulated by Au and partially dissolved into the subsurface, leaving behind isolated Pd monomers on the surface. Subsequent exposure to 0.1 mbar CO enabled Pd monomers to repopulate the surface up to 373 K, above which complete Pd dissolution occurred by 473 K, with apparent activation energies of 0.14 and 0.48 eV, respectively. These restructuring processes occurred over the span of ∼1000 s at a given temperature. Such a minute-timescale dynamics not only elucidates the fluxional nature of alloy catalysts but also presents an opportunity to fine-tune the surface under moderate temperature and pressure conditions.

Migrative Carbofluorination of Saturated Amides Enabled by Pd-Based Dyotropic Rearrangement

Directly editing an all-carbon quaternary carbon itself of nonstrained acyclic molecules remains underexploited despite the recent advances in the fields of both C-H and C-C bond activation. Herein, we report a palladium-catalyzed migrative carbofluorination of saturated amides enabled by the activation of both the C(sp³)-H and the C_quaternary-Cσ bonds. In this transformation, the α-quaternary carbon of Weinreb amides is converted to α-tertiary fluoride with concurrent migration of an aryl or an amido group from the α- to β-carbon. DFT calculations indicate that the dyotropic rearrangement proceeds through an unusual anti-selective [2.1.0] bicyclic transition state. The reaction, compatible with a broad range of functional groups, is stereospecific and is applicable to the synthesis of enantioenriched products.

The structural and electronic richness of buckled honeycomb AsP bilayers

The sixteen different high-symmetry stacking configurations in buckled honeycomb AsP bilayers were identified using block diagrams and studied through several high-level computations, including the adiabatic-connection fluctuation-dissipation theorem in the random phase approximation (ACFDT-RPA). The lowest-lying energy form is an AA-type stacking, which is an indirect bandgap semiconductor, according to the G₀W₀ approach. All bilayers are indirect wide bandgap semiconductors, except for two systems, a narrow bandgap semiconductor and one with metallic behavior. This study shows the richness of structural and electronic properties in AsP hetero-bilayers with configurations found over a broad spectrum of interlayer distances and bandgaps.

Grazing incidence fast atom and molecule diffraction: theoretical challenges

This perspective article reviews the state-of-the-art of grazing incidence fast atom and molecule diffraction (GIFAD and GIFMD) simulations and addresses the main challenges that theorists, aiming to provide useful inputs in this topic, are facing. We first discuss briefly the methods used to build accurate potential energy surfaces describing the interaction between the projectile and the surface. Subsequently, we focus on the dynamics simulation methods for GIFAD, a phenomenon that has received a lot of experimental attention since 2007, when the first measurements were published. Following this experimental effort, theorists have developed and adapted a bunch of methods able to simulate, analyze and extract information from the experimental outputs. We review these methods, from the very simple ones based on classical dynamics to the full quantum ones, paying special attention to more versatile semiclassical approaches, which include quantum ingredients in the dynamics at a computational cost only slightly higher than that required in classical dynamics. Within the semiclassical framework it is possible, for example, to include in the dynamics the surface phonons and the projectile coherence, two factors that may have a relevant influence on the experimental measurements, at a reasonable computational cost. Finally, we address GIFMD, a phenomenon that has received much less attention and for which there is still a lot of room for research. We review the few examples of GIFMD available in the literature, and we discuss new phenomena associated with the molecular internal degrees of freedom, which may have some impact in other closely related fields, such as molecular reactivity on metal surfaces. Finally, we point out opened questions, raised from the comparisons between theoretical and experimental results, which claim for further experimental efforts.

Ultrafast Vibrational Response of Activated C-D Bonds in a Chloroform-Platinum(II) Complex

The vibrational response of the activated C-D bond in the chloroform complex [Pt(C₆H₅)₂(btz-N,N')·CDCl₃, where btz = 2,2'-bi-5,6-dihydro-4H-1,3-thiazine] is studied by linear and nonlinear two-dimensional infrared (2D-IR) spectroscopy. The change of the C-D stretching vibration of metal-coordinated CDCl₃ relative to the free solvent molecule serves as a measure of the non-classical Pt···D-C interaction strength. The stretching absorption band of the activated C-D bond displays a red shift of 119 cm^-1 relative to uncoordinated CDCl₃, a strong broadening, and an 8-fold enhancement of spectrally integrated absorption. The infrared (IR) absorption and 2D-IR line shapes are governed by spectral diffusion on 200 fs and 2 ps time scales, induced by the fluctuating solvent CDCl₃. The enhanced vibrational absorption and coupling to solvent forces are assigned to the enhanced electric polarizability of the activated C-D bond. Density functional theory calculations show a significant increase of C-D bond polarizability of CDCl₃ upon coordination to the 16 valence electron Pt(II) complex.

First-Principles Study of Three-Dimensional Electrides Containing One-Dimensional [Ba3N]3+ Chains

Electrides, a unique type of compound where electrons act as anions, have a high electron mobility and a low work function, which makes them promising for applications in electronic devices and high-performance catalysts. The discovery of novel electrides and the expansion of the electride family have great significance for their promising applications. Herein, we reported four three-dimensional (3D) electrides by coupling crystal structure database searches and first-principles electronic structure analysis. Subnitrides (Ba₃N, LiBa₃N, NaBa₃N, and Na₅Ba₃N) containing one-dimensional (1D) [Ba₃N]³⁺ chains are identified as 3D electrides for the first time. The anionic electrons are confined in the 3D interstitial space of Ba₃N, LiBa₃N, NaBa₃N, and Na₅Ba₃N. Interestingly, with the increase of Na content, the excess electrons of Na₅Ba₃N play two roles of metallic bonding and anionic electrons. Therefore, the subnitrides containing 1D [Ba₃N]³⁺ chains can be regarded as a new family of 3D electrides, where anionic electrons reside in the 3D interstitial spaces and provide a conduction path. These materials not only are experimentally synthesizable 3D electrides but also are promising to be exfoliated into advanced 1D nanowire materials. Furthermore, our work suggests a discovery strategy of novel electrides based on one parent framework like [Ba₃N]³⁺ chains, which would accelerate the mining of electrides from the crystal structure database.

Assessing the persistence of chalcogen bonds in solution with neural network potentials

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environment effects, which promote competing interactions and alter their static gas-phase properties. Recently, neural network potentials (NNPs) trained on Density Functional Theory (DFT) data have become increasingly popular to simulate molecular phenomena in condensed phase with an accuracy comparable to ab initio methods. To date, most applications have centered on solid-state materials or fairly simple molecules made of a limited number of elements. Herein, we focus on the persistence and strength of chalcogen bonds involving a benzotelluradiazole in condensed phase. While the tellurium-containing heteroaromatic molecules are known to exhibit pronounced interactions with anions and lone pairs of different atoms, the relevance of competing intermolecular interactions, notably with the solvent, is complicated to monitor experimentally but also challenging to model at an accurate electronic structure level. Here, we train direct and baselined NNPs to reproduce hybrid DFT energies and forces in order to identify what are the most prevalent non-covalent interactions occurring in a solute-Cl$^-$-THF mixture. The simulations in explicit solvent highlight competition with chalcogen bonds formed with the solvent and the short-range directionality of the interaction with direct consequences for the molecular properties in the solution. The comparison with other potentials (e.g., AMOEBA, direct NNP and continuum solvent model) also demonstrates that baselined NNPs offer a reliable picture of the non-covalent interaction interplay occurring in solution.

Local Kernel Regression and Neural Network Approaches to the Conformational Landscapes of Oligopeptides

The application of machine learning to theoretical chemistry has made it possible to combine the accuracy of quantum chemical energetics with the thorough sampling of finite-temperature fluctuations. To reach this goal, a diverse set of methods has been proposed, ranging from simple linear models to kernel regression and highly nonlinear neural networks. Here we apply two widely different approaches to the same, challenging problem: the sampling of the conformational landscape of polypeptides at finite temperature. We develop a local kernel regression (LKR) coupled with a supervised sparsity method and compare it with a more established approach based on Behler-Parrinello type neural networks. In the context of the LKR, we discuss how the supervised selection of the reference pool of environments is crucial to achieve accurate potential energy surfaces at a competitive computational cost and leverage the locality of the model to infer which chemical environments are poorly described by the DFTB baseline. We then discuss the relative merits of the two frameworks and perform Hamiltonian-reservoir replica-exchange Monte Carlo sampling and metadynamics simulations, respectively, to demonstrate that both frameworks can achieve converged and transferable sampling of the conformational landscape of complex and flexible biomolecules with comparable accuracy and computational cost.

The Adsorption of Small Molecules on the Copper Paddle-Wheel: Influence of the Multi-Reference Ground State

We report a theoretical study of the adsorption of a set of small molecules (C2H2, CO, CO2, O2, H2O, CH3OH, C2H5OH) on the metal centers of the "copper paddle-wheel"-a key structural motif of many MOFs. A systematic comparison between DFT of different rungs, single-reference post-HF methods (MP2, SOS-MP2, MP3, DLPNO-CCSD(T)), and multi-reference approaches (CASSCF, DCD-CAS(2), NEVPT2) is performed in order to find a methodology that correctly describes the complicated electronic structure of paddle-wheel structure together with a reasonable description of non-covalent interactions. Apart from comparison with literature data (experimental values wherever possible), benchmark calculations with DLPNO-MR-CCSD were also performed. Despite tested methods show qualitative agreement in the majority of cases, we showed and discussed reasons for quantitative differences as well as more fundamental problems of specific cases.

Structural Properties and Magnetic Ground States of 100 Binary d-Metal Oxides Studied by Hybrid Density Functional Methods

d-metal oxides play a crucial role in numerous technological applications and show a great variety of magnetic properties. We have systematically investigated the structural properties, magnetic ground states, and fundamental electronic properties of 100 binary d-metal oxides using hybrid density functional methods and localized basis sets composed of Gaussian-type functions. The calculated properties are compared with experimental information in all cases where experimental data are available. The used PBE0 hybrid density functional method describes the structural properties of the studied d-metal oxides well, except in the case of molecular oxides with weak intermolecular forces between the molecular units. Empirical D3 dispersion correction does not improve the structural description of the molecular oxides. We provide a database of optimized geometries and magnetic ground states to facilitate future studies on the more complex properties of the binary d-metal oxides.

Mechanistic and Electronic Insights into a Working NiAu Single-Atom Alloy Ethanol Dehydrogenation Catalyst

Elucidation of reaction mechanisms and the geometric and electronic structure of the active sites themselves is a challenging, yet essential task in the design of new heterogeneous catalysts. Such investigations are best implemented via a multipronged approach that comprises ambient pressure catalysis, surface science, and theory. Herein, we employ this strategy to understand the workings of NiAu single-atom alloy (SAA) catalysts for the selective nonoxidative dehydrogenation of ethanol to acetaldehyde and hydrogen. The atomic dispersion of Ni is paramount for selective ethanol to acetaldehyde conversion, and we show that even the presence of small Ni ensembles in the Au surface results in the formation of undesirable byproducts via C-C scission. Spectroscopic, kinetic, and theoretical investigations of the reaction mechanism reveal that both C-H and O-H bond cleavage steps are kinetically relevant and single Ni atoms are confirmed as the active sites. X-ray absorption spectroscopy studies allow us to follow the charge of the Ni atoms in the Au host before, under, and after a reaction cycle. Specifically, in the pristine state the Ni atoms carry a partial positive charge that increases upon coordination to the electronegative oxygen in ethanol and decreases upon desorption. This type of oxidation state cycling during reaction is similar to the behavior of single-site homogeneous catalysts. Given the unique electronic structure of many single-site catalysts, such a combined approach in which the atomic-scale catalyst structure and charge state of the single atom dopant can be monitored as a function of its reactive environment is a key step toward developing structure-function relationships that inform the design of new catalysts.

Adsorption of CH4 on the Pt(111) surface: Random phase approximation compared to density functional theory

We investigate the adsorption of CH₄ on the Pt(111) surface for two adsorption modes, hcp (hexagonal closed packed) hollow tripod and top monopod in a (√3 × √3)R30° surface cell that corresponds to experimental surface coverage. Surface structures are optimized with density functional theory using the Perdew-Burke-Ernzerhof (PBE) functional augmented with the many-body dispersion scheme of Tkatchenko (PBE+MBD). Whereas the Random Phase Approximation (RPA) predicts a clear preference of about 5 kJ mol^-1 for the hcp tripod compared to the top monopod structure, in agreement with vibrational spectra, PBE+MBD predicts about equal stability for the two adsorption structures. For the hcp tripod, RPA yields an adsorption energy of -14.5 kJ mol^-1, which is converged to within 1.0 ± 0.5 kJ mol^-1 with respect to the plane wave energy cutoff (500 eV), the k-point mesh (4 × 4 × 1), the vacuum layer (about 10.3 Å, with extrapolation to infinite distance), and the number of Pt layers (3). Increments for increasing the number of Pt layers to 4 (+1.6 kJ mol^-1) and the k-point mesh to 6 × 6 × 1 (-0.6 kJ mol^-1) yield a final estimate of -13.5 ± 2.1 kJ mol^-1, which agrees to within 2.2 ± 2.1 kJ mol^-1 with experiment (-15.7 ± 1.6), well within the chemical accuracy range.

Chemically Activating Tungsten Disulfide via Structural and Electronic Engineering Strategy for Upgrading the Hydrogen Evolution Reaction

Both improving the intrinsic activity and activating basal plane sites of the layered metal dichalcogenides are desirable to enhance their electrocatalytic performance for energy storage and conversion. Herein, we present palladium (Pd)-doped tungsten disulfide (WS₂) epitaxially sheathed around linear tungsten oxide for the hydrogen evolution reaction (HER). The Pd doping is evidenced to tune the electronic structure of WS₂ for activating basal sites of WS₂, while the unique core-shell structure facilitates charge transfer. The as-prepared Pd-WS₂/W₃O with 5.65 wt % Pd content exhibits a small overpotential of only 54 mV at -10 mA cm^-2 and superior stability in the acidic electrolyte, which are superior to that of the 5 wt % Pt/C benchmark and are unprecedented in the reported WS₂-based electrocatalysts. Theoretical results have revealed that Pd substituting for W in coordination with four S atoms is thermodynamically stable, and the in-plane S atoms adjacent to the doped Pd represent new catalytic active centers for promoting hydrogen adsorption. This work provides a new multiscale structural and electronic engineering strategy for improving the catalytic performance of transition-metal dichalcogenides.

Surface Chemistry of MoS2 in Remote Oxygen Plasma

Miniaturization of electronic devices down to the nanoscale needs corresponding processing technologies with precision at the atomic layer level. The plasma atomic layer etching (ALE) technique is playing an active role in this demand. However, theoretical research on the ALE mechanism is a great challenge. We propose a method of spontaneously searching adsorption sites (SSASs) to understand what surface chemistry occurs in the ALE processing of MoS₂ treated by the remote oxygen plasma. The SSAS results are in good agreement with experimental observations. Chemical adsorption of O atoms occurs only in the topmost layer of the MoS₂ surface. The MoS₂ surface has four different adsorption sites with different probabilities of binding an O atom, denoted by 0Sbb, 0Sbbc, 2Sbb, and 3Sbb configurations, which have zero, zero, two, and three S-Mo bonds broken by the introduced O atom, respectively. Four adsorption sites of the MoS₂ surface play different roles in the surface oxidation in the remote oxygen plasma.

Mechanical and Chemical Interactions in Atomically Defined Contacts

Providing fundamental insights in atomic interactions, dedicated methods in atomic force microscopy allow measuring the threshold forces needed to move single adsorbed atoms or molecules. However, the chemical and structural properties of the probe-tip can drastically influence the results. Establishing atomically defined contacts in such experiments, the tips in the present study are functionalized with various chemically and structurally different terminations. Xenon atoms are moved along an atomically defined metal/metal-oxide boundary where all tips show a pulling mechanism and slight force variations, which are assigned to polarization effects within the tip-sample junction. Detaching Xe atoms from the boundary involves a significantly higher energy barrier where chemical reactive Cu-tips cause Xe pickup before any lateral manipulation. Passivating the tip by inert probe particles (Xe or CO) allows further approaching the surface Xe atom. Yet, the small vertical attraction and pronounced tip relaxations prevent reaching sufficient threshold forces inducing manipulation. In contrast, the high structural rigidity of oxygen-terminated Cu-tips allows manipulations even beyond the threshold where they evolve from initial pulling, via sliding to pushing mode. The detailed quantitative analysis of the processes in the atomically defined junctions emphasizes the mechanical and chemical interactions for highly controlled experiments with piconewton sensitivity.