A comparative study on the linear scaling relations for the diffusion of S-vacancies on MoS2 and WS2.

This work uses density functional theory (DFT) calculations and kinetic Monte Carlo (kMC) simulations to compare the diffusion of S-vacancies on defective MoS2 and WS2, two structures that are often discussed as catalysts. Similar to what has been discussed for MoS2, the vacancy diffusion barriers on WS2 also follow Brønsted-Evans-Polanyi (BEP) type linear scaling relations. The vacancy diffusion kinetics is discussed at the example of a large vacancy cluster consisting of 37 unoccupied sites in direct vicinity and how its structure changes with time. Using barriers estimated via linear scaling relations as input for the kMC simulations yields results that qualitatively agree with results calculated self-consistently at DFT level. As the diffusion barriers for WS2 are significantly higher than those for MoS2, the vacancy diffusion on WS2 is poorly described by the linear scaling relations derived from MoS2 and vice versa. This work further shows that one needs DFT level barriers of about 40% of all S-vacancy diffusion processes on a material to derive sufficiently reliable linear scaling relations. This means that computational costs for future studies may be reduced by only explicitly computing one fraction of the diffusion barriers while estimating the remaining ones via linear scaling. However, in this case, one would lack information about the partition function of the transition states, which are needed for calculating the rate constants. Thus, we have also proposed a scheme to estimate the contribution of the partition functions based only on the initial state's vibrational modes.

Correction: First-principles modeling of the highly dynamical surface structure of a MoS2 catalyst with S-vacancies.

Correction for 'First-principles modeling of the highly dynamical surface structure of a MoS2 catalyst with S-vacancies' by Po-Yuan Wang et al., Phys. Chem. Chem. Phys., 2022, 24, 24166-24172, https://doi.org/10.1039/D2CP03384D.

First-principles modeling of the highly dynamical surface structure of a MoS2 catalyst with S-vacancies.

Vacancy sites, e.g., S-vacancies, are essential for the performance of MoS2 catalysts. As earlier studies have revealed that the size and shape of the S-vacancies may affect the catalytic activity, we have studied the behavior and mobility of such vacancies on MoS2 using DFT calculations and kinetic Monte-Carlo (kMC) simulations. The diffusion barriers for the S-vacancies are highly dependent on the immediate environment: isolated single S-vacancies are found to be immobile. In contrast, small nS-vacancies formed from n = 2 to 5 neighboring S-vacancies are often highly dynamic systems that can move within a confined area. Large extended nS-vacancies are generally unstable and transform quickly into alternating patterns of S-atoms and vacancy sites. These results illustrate the importance of recognizing MoS2 (but also other catalysts) as dynamic structures when trying to tune their catalytic performances by introducing specific defect structures.

Collision-induced dissociation of Na+-tagged ketohexoses: experimental and computational studies on fructose.

Collision-induced dissociation tandem mass spectrometry (CID-MSn) and computational investigation at the MP2/6-311+G(d,p) level of theory have been employed to study Na+-tagged fructose, an example of a ketohexose featuring four cyclic isomers: α-fructofuranose (αFruf), ß-fructofuranose (ßFruf), α-fructopyranose (αFrup), and ß-fructopyranose (ßFrup). The four isomers can be separated by high-performance liquid chromatography (HPLC) and they show different mass spectra, indicating that CID-MSn can distinguish the different fructose forms. Based on a simulation using a micro-kinetic model, we have obtained an overview of the mechanisms for the different dissociation pathways. It has been demonstrated that the preference for the C-C cleavage over the competing isomerization of linear fructose is the main reason for the previously reported differences between the CID-MS spectra of aldohexoses and ketohexoses. In addition, the kinetic modeling helped to confirm the assignment of the different measured mass spectra to the different fructose isomers. The previously reported assignment based on the peak intensities in the HPLC chromatogram had left some open questions as the preference for the dehydration channels did not always follow trends previously observed for aldohexoses. Setting up the kinetic model further enabled us to directly compare the computational and experimental results, which indicated that the model can reproduce most trends in the differences between the dissociation pathways of the four cyclic fructose isomers.

Aromatization as an Impetus to Harness Ketones for Metallaphotoredox-Catalyzed Benzoylation/Benzylation of (Hetero)arenes.

Herein we report ketones as feedstock materials in radical cross-coupling reactions under Ni/photoredox dual catalysis. In this approach, simple condensation first converts ketones into prearomatic intermediates that then act as activated radical sources for cross-coupling with aryl halides. Our strategy enables the direct benzylation/benzoylation of (hetero)arenes under mild reaction conditions with high functional group tolerance.

A decomposition mechanism for Mn2(DSBDC) metal-organic frameworks in the presence of water molecules.

In this work, we investigate the effects of water on the structural stability of Mn2(DSBDC) metal-organic framework (MOF) using DFT-based calculations. It has been found that the adsorption of multiple water molecules forming a hydrogen bond network around the Mn centers plays an important role in the decomposition process. Different effects contribute to the destabilization of the MOF: water molecules that directly coordinate to the open sites displayed by a part of the Mn centers can induce a significant shift in the charge distribution as indicated by the analysis of charge density differences and the Bader charges. This adsorption process leads to a slight elongation of the metal-linker bonds. The direct interaction with the Mn center is the most stable adsorption mode for water in Mn2(DSBDC). Once these adsorption sites at the Mn centers are fully occupied, additional water molecules start to bind via hydrogen bonds to the already present water molecules or, more importantly, to the linker molecules. This, in return, leads to a significant weakening of the Mn-linker bonds, thus allowing water insertion into the Mn-linker bonds with a barrier of only 0.16 eV, which is believed to initiate the decomposition of the Mn2(DSBDC) framework. Based on a kinetic Monte Carlo model, it can be shown that high temperatures can prevent the adsorption of water molecules around the Mn sites and thus slow down the MOF decomposition.

Cobalt Iron Oxides Prepared by Acidic Redox-Assisted Precipitation: Characterization, Applications, and New Opportunities.

The microscopic homogeneity of mixed metals in a single-phase oxide is a critical issue in improving material performance. Aqueous alkaline precipitation is the most common approach but it has the limits of microscopic inhomogeneity because of intrinsically different precipitation rates between metal cations. Herein, we demonstrate a new preparation of uniformly structural substituted cobalt iron oxides via acidic redox-assisted precipitation (ARP) upon the interaction of CoII and K2FeO4. This low-pH synthesis features the redox process between Co and Fe, presumably through the formation of inner-sphere complexes such as [(H2O)5CoII-O-FeVIO3]. With the nucleation starting from such complexes, one obtains a product with predominantly mixed-metal Co-O-Fe moieties, which improves the electrical conductivity of the product. This work further analyzes how the properties of the product species evolve during the hydrothermal synthesis step in the ARP process. We see that the Co/Fe ratio slowly increases from about 1:1 to a final value of 2:1, but does not reach the expected redox stoichiometry of 3:1. At the same time, the magnetization also increases, reaching a value of 16.9 emu g-1 for the final superparamagnetic product, which is three times higher than the value of monometallic Co3O4 and Fe2O3. The cobalt iron oxide samples obtained from ARP also possess superior oxygen evolution activity (307 mV overpotential at 10 mA cm-2 µg-1) compared to a mixture of Co3O4 and Fe2O3 (422 mV) or pure cobalt oxide (350 mV), highlighting the structure-induced enhancement of the catalytic activity. The difficult synthesis of evenly blended trinary/quaternary metals in a single-oxide phase may become possible in the future via ARP.

Improved agreement between experimental and computational results for collision-induced dissociation mass spectrometry of cation-tagged hexoses.

To model the collision-induced dissociation mass spectrometry (CID-MS) of Na+-tagged hexoses, it is not only required to perform an extensive sampling of the conformational space as addressed in our previous work [Huynh et al., Phys. Chem. Chem. Phys., 2018, 20(29), 19614-19624], it is also necessary to apply a sufficiently reliable quantum chemical method to describe the relative energetics of the reactions. In this work, the ring-opening via hemiacetal scission and the competing dehydration pathways have been re-evaluated at the MP2 level. The results show that previous studies at the B3LYP level display a systematic underestimation of the dehydration barriers by about 40 kJ mol-1 on average while the ring-opening barriers are reasonably described. We further illustrate that, in the present case, it is not enough to only look at the energetics: although MP2 results indicate that the ring-opening pathways of the considered hexoses have lower barriers than the dehydration pathways, the contributions of the partition functions to the rate constants render the dehydration for some structures to be more favorable at elevated temperatures. Via benchmark calculations against single-point CCSD(T) results at the example of small organic model molecules, we demonstrate that the MP2 data for the studied reactions are, alongside calculations at the M06-2X level, trustworthy. In addition, we have analyzed for the same set of model molecules how the fraction of exact exchange in the applied exchange-correlation functional affects the reaction barriers and the charge distributions. While MP2 (and M06-2X) calculations indicate an increased charge localization when going from the initial state to the dehydration transition state, this phenomenon is not seen in the B3LYP calculations, which likely is the origin of the discrepancy between the B3LYP and MP2 dehydration barriers. As the variation of the charge localization during a hemiacetal scission reaction is comparably small, B3LYP performs sufficiently well for such reactions.

From the perspectives of DFT calculations, thermodynamic modeling, and kinetic Monte Carlo simulations: the interaction between hydrogen and Sc2C monolayers.

In this study, we have examined the adsorption properties of hydrogen on pristine Sc2C monolayers by DFT calculations. Based on these calculations, we have proposed a thermodynamic model to estimate the hydrogen storage capability within the typical ranges for the operating temperature and pressure. Our thermodynamic modeling has shown that the maximum uptake of usable hydrogen could reach up to 7.2 wt% under cryogenic conditions. When calculating the usable hydrogen uptake, we have taken into consideration that, under realistic operating conditions, not all hydrogen adsorbed on pristine Sc2C can be desorbed from the surface, as some surface-adsorbate interactions are too strong. On the other hand, the interaction between the usable hydrogen and Sc2C appears to be too weak to reach the targets for the year 2025 set by the US Department of Energy (5.5 wt% at operating temperatures between 233 K and 358 K and delivery pressures of up to 12 bar). According to the modeling results, one needs to decrease the temperature to 120 K to reach 5.5 wt% hydrogen uptake at 12 bar. The results obtained with the thermodynamic model have been confirmed with a kinetic Monte Carlo simulation, which has also been used to estimate the time scale of the hydrogen adsorption and desorption processes. In addition, we have also evaluated the changes in the electronic structure of the Sc2C monolayer upon adsorbing hydrogen. As the band gap of Sc2C changes significantly upon adsorbing H2, Sc2C may have more potential as a hydrogen detector instead of as a hydrogen storage material.

Influence of nonmetal dopants on charge separation of graphitic carbon nitride by time-dependent density functional theory.

Photocatalysts are crucial materials for green energy production and environmental remediation. Nonmetal-doped graphitic carbon nitride (g-C3N4) has attracted much attention in recent years because of its low-cost and desired photocatalytic performances, such as a high charge separation efficiency and broad visible light absorption. In this study, we conducted time-dependent density functional theory calculations, and a wavefunction analysis to evaluate the charge separation characteristics of phosphorus-, oxygen- and sulfur-doped g-C3N4 upon photo-excitation. In particular, we examined the electron-hole pair distances, the electron-hole pair overlaps, and the amounts of transferred charge. The phosphorus, oxygen, and sulfur dopants shifted the lowest unoccupied molecular orbital of doped heptazine rings downward to facilitate the electron transfer upon photo-excitation. Generally, the phosphorus dopant triggers relatively high amounts of transferred charge, strong electron-hole pair separations, and low electron-hole overlaps compared to oxygen and sulfur dopants. At a low dopant concentration, the sulfur dopant showed a similar effect to that of the phosphorus dopant. The phosphorus dopants not only contributed to the electron-hole pair separation, but also attracted photo-excited electrons. The comparison of different dopant distributions on the heptazine rings of g-C3N4 showed that dopants concentrated on one heptazine ring exhibit better charge separation performance than dopants dispersed on different heptazine rings do. This indicates that the doping configuration has a stronger effect than the doping concentration on the charge separation efficiency in nonmetal-doped g-C3N4.

Toward Closing the Gap between Hexoses and N-Acetlyhexosamines: Experimental and Computational Studies on the Collision-Induced Dissociation of Hexosamines.

Motivated by the fundamental difference in the reactivity of hexoses and N-acetylhexosamines under collision-induced dissociation (CID) mass spectrometry conditions, we have investigated the CID of two hexosamines, glucosamine (GlcN) and galactosamine (GalN), experimentally and computationally. Both hexosamines undergo ring-opening and then dissociate via the 0,2A and the 0,3A (0,3X) cross-ring cleavage channels. The preference for the ring-opening is similar to the behavior of N-acetylhexosamines and explains why the two anomers of the same sugar give the same mass spectrum. While the spectrum for GlcN is dominated by the 0,2A signal, the signal intensities for both 0,2A and the 0,3A (0,3X) dissociation channels are comparable for GalN, which allows GlcN and GalN to be distinguished easily. Calculations at MP2 level of theory indicate that this is related to the differences in the relative barrier heights for the 0,2A and the 0,3A (0,3X) cross-ring cleavage channels. This, in return, reflects the circumstance that the 0,2A cross-ring cleavage barriers are different for the two sugars, while the barriers of all other dissociation channels are comparable. While the mechanisms of the cross-ring dissociation channels of hexoses are well described using the retro-aldol mechanism in the literature, this study proposes a new mechanism for the 0,3A (0,3X) cross-ring cleavage of hexosamines that involves the formation of an epoxy intermediate or a zwitterionic intermediate.

Unexpected Dissociation Mechanism of Sodiated N-Acetylglucosamine and N-Acetylgalactosamine.

The mechanism for the collision-induced dissociation (CID) of two sodiated N-acetylhexosamines (HexNAc), N-acetylglucosamine (GlcNAc), and N-acetylgalactosamine (GalNAc), was studied using quantum-chemistry calculations and resonance excitation in a low-pressure linear ion trap. Experimental results show that the major dissociation channel of the isotope labeled [1-18O, D5]-HexNAc is the dehydration by eliminating HDO, where OD comes from the OD group at C3. Dissociation channels of minor importance include the 0,2A cross-ring dissociation. No difference has been observed between the CID spectra of the α- and ß-anomers of the same HexNAc. At variance, the CID spectra of GlcNAc and GalNAc showed some differences, which can be used to distinguish the two structures. It was observed in CID experiments involving disaccharides with a HexNAc at the nonreducing end that a ß-HexNAc shows a larger dissociation branching ratio for the glycosidic bond cleavage than the α-anomer. This finding can be exploited for the rapid identification of the anomeric configuration at the glycosidic bond of HexNAc-R' (R' = sugar) structures. The experimental observations indicating that the dissociation mechanisms of HexNAcs are significantly different from those of hexoses were explained by quantum-chemistry calculations. Calculations show that ring opening is the major channel for HexNAcs in a ring form. After ring opening, dehydration shows the lowest barrier. In contrast, the glycosidic bond cleavage becomes the major channel for HexNAcs at the nonreducing end of a disaccharide. This reaction has a lower barrier for ß-HexNAcs as compared with the barrier of the corresponding α-anomers, consistent with the higher branching ratio for ß-HexNAcs observed in experiment.

Structures and infrared spectra of calcium phosphate clusters by ab initio methods with implicit solvation models.

Since the first detection of pre-nucleation clusters during the formation of calcium phosphate minerals, determining such clusters' compositions and structures has become crucial for understanding the early-stage nucleation of these minerals in solutions. In previous experimental studies, the composition and sizes of pre-nucleation clusters have been calculated, but their structural information has been difficult to determine because they are very small (<1 nm). In this study, we examined the structures and infrared spectra of small- and medium-sized calcium phosphate clusters using ab initio calculations combined with implicit solvation models. Adding solvent effects increased the possibility of the existence of alternative configurations of calcium phosphate clusters other than their compact configurations. The calcium atoms had a tendency to be located outside of the clusters to coordinate with water molecules in the aqueous environment. The computed infrared spectra of extended small calcium phosphate clusters captured some of the features measured in the in situ infrared spectra, which supports the network structures proposed by large-scale molecular dynamics studies and X-ray adsorption near-edge spectra. The relative stabilities of medium-sized Ca9(PO4)6 clusters with respect to the stability of Posner's cluster in water were also reviewed. We found that in water, alternative structures with low symmetry or large dipole moments had lower energies than Posner's cluster.

Tuning the vibrational coupling of H3O+ by changing its solvation environment.

This study demonstrates how the intermode coupling in the hydronium ion (H3O+) is modulated by the composition of the first solvation shell. A series of rare gas solvated hydronium ions (H3O+Rg3, where Rg = Ne, Ar, Kr, and Xe) is examined via reduced-dimensional anharmonic vibrational (RDAV) ab initio calculations. We considered six key vibrational normal modes, namely: a hindered rotation, two H-O-H bends, and three O-H stretches. Between the O-H stretches and the H-O-H bends, the first is more sensitive to solvation strength. Our calculations revealed that the Fermi resonance between the first overtones of O-H bends and the fundamentals of O-H stretches led to complex spectral features from 3000 to 3500 cm-1. Such an interaction is not only sensitive to the type of rare gas messengers surrounding the H3O+ ion, it also exhibits an anomalous H → D isotope effect. Although it is accepted that visible combination tones (∼1900 cm-1) arise from the complex coupling between the hindered rotation and the H-O-H bends, the origin of their intensities is not yet clearly understood. We found that the intensity of these combination tones could be much stronger than their fundamental H-O-H bends. Within our theoretical framework, we tracked the combination tone's intensity back to the asymmetric O-H stretches. This simple notion of intensity borrowing is confirmed by examining eight complexes (H3O+·Rg3 and D3O+·Rg3) with spectral features awaiting experimental confirmations.

Tunable Gravimetric and Volumetric Hydrogen Storage Capacities in Polyhedral Oligomeric Silsesquioxane Frameworks.

We study the hydrogen adsorption in porous frameworks composed of silsesquioxane cages linked via boron substituted aromatic structures by first-principles modeling. Such polyhedral oligomeric silsesquioxane (POSS) frameworks can be further modified by decorating them with metal atoms binding to the ring structures of the linkers. We have considered Sc- and Ti-doped frameworks which bind H2 via so-called Kubas interaction between hydrogen molecules and transition metal atoms. It will be demonstrated that the maximum H2 gravimetric capacity can be improved to more than 7.5 wt % by using longer linkers with more ring structures. However, the maximum H2 volumetric capacity can be tuned to more than 70 g/L by varying the size of silsesquioxane cages. We are optimistic that by varying the building blocks, POSS frameworks can be modified to meet the targets for the gravimetric and volumetric capacities set by the U.S. Department of Energy.

Transformations of Organic Molecules over Metal Surfaces: Insights from Computational Catalysis.

Much-needed progress in catalytic science, in particular regarding heterogeneous catalysis, is associated with the transition from largely empirical research to rational design of new and improved catalysts and catalytic processes. To achieve this goal, fundamental atomic-scale understanding of catalytic processes is required, which can be achieved with the help of theoretical modeling, in particular, using methods based on quantum chemical calculations. In this review we illustrate the current progress by discussing examples from the authors' work in which complex reaction networks involving organic molecules on transition-metal surfaces have been studied using density functional theory. We review some of the success stories where theory helped to interpret experimental observations and provided atomistic insights into the mechanisms, which were not definitively known before. In other cases, partial disagreement between theoretical results and existing experimental evidence calls for further reconciliation studies.

Structure and electronic properties of MoVO type mixed-metal oxides - a combined view by experiment and theory.

In this review we address recent efforts from experimental and theoretical side to study MoVO-type mixed metal oxides (MMOs) and their properties. We illustrate how structures of MMOs have been evaluated using a large variety of experimental techniques, such as electron microscopy, neutron diffraction, and X-ray diffraction. Furthermore, we discuss the current view on structure-catalysis correlations, derived from recent experiments. In a second part, we examine useful tools of theoretical chemistry for exploring MoVO-type systems. We discuss the need for using hybrid DFT methods and we analyze how, in the context of MMOs studies, semi-local DFT approximations can encounter problems due to a notable self-interaction error when describing oxidic species and reactions on them. In addition, we discuss various aspects of the model that are important when attempting to map complex MMO systems.

C-O cleavage of aromatic oxygenates over ruthenium catalysts. A computational study of reactions at step sites.

We studied the C-O cleavage of phenolate and catecholate at step sites of a Ru catalyst using periodic DFT methods at the GGA level. Both C-O scission steps are associated with activation barriers of about 75 kJ mol(-1), hence are significantly more facile than the analogous reactions on Ru terraces. With these computational results, we offer an interpretation of recent experiments on the hydrodeoxygenation of guaiacol (2-methoxyphenol) over Ru/C. We hypothesize that the experimentally observed dependency of the product selectivity on the H2 pressure is related to the availability of step sites on a Ru catalyst.

Molecular understandings on the activation of light hydrocarbons over heterogeneous catalysts.

Due to the depletion of petroleum and the recent shale gas revolution, the dropping of the price for light alkanes makes alkanes an attractive feedstock for the production of light alkenes and other valuable chemicals. Understanding the mechanism for the activation of C-H bonds in hydrocarbons provides fundamental insights into this process and a guideline for the optimization of catalysts used for the processing of light alkanes. In the last two decades, density functional theory (DFT) has become a powerful tool to explore elementary steps and mechanisms of many heterogeneously catalyzed processes at the atomic scale. This review describes recent progress on computational understanding of heterogeneous catalytic dehydrogenation reactions of light alkanes. We start with a short description on basic concepts and principles of DFT as well as its application in heterogeneous catalysis. The activation of C-H bonds over transition metal and alloy surfaces are then discussed in detail, followed by C-H activation over oxides, zeolites and catalysts with single atoms as active sites. The origins of coking formation are also discussed followed by a perspective on directions of future research.

Predicting adsorption enthalpies on silicalite and HZSM-5: A benchmark study on DFT strategies addressing dispersion interactions.

We evaluated the accuracy of periodic density functional calculations for adsorption enthalpies of water, alkanes, and alcohols in silicalite and HZSM-5 zeolites using a gradient-corrected density functional with empirical dispersion corrections (PBE-D) as well as a nonlocal correlation functional (vdW-DF2). Results of both approaches agree in acceptable fashion with experimental adsorption energies of alcohols in silicalite, but the adsorption energies for n-alkanes in both zeolite models are overestimated, by 21-46 kJ mol(-1). For PBE-D calculations, the adsorption of alkanes is exclusively determined by the empirical dispersion term, while the generalized gradient approximation-DFT part is purely repulsive, preventing the molecule to come too close to the zeolite walls. The vdW-DF2 results are comparable to those of PBE-D calculations, but the latter values are slightly closer to the experiment in most cases. Thus, both computational approaches are unable to reproduce available experimental adsorption energies of alkanes in silicalite and HZSM-5 zeolite with chemical accuracy.