Application of Automated Reaction Path Search Methods to a Systematic Search of Single-Bond Activation Pathways Catalyzed by Small Metal Clusters: A Case Study on H–H Activation by Gold

An automated reaction route mapping for the reaction of NO and active species on Ag4 clusters in zeolites

A computational investigation of the catalytic reaction on multinuclear sites is very challenging. Here, using an automated reaction route mapping method, the single-component artificial force induced reaction (SC-AFIR) algorithm, the catalytic reaction of NO and OH/OOH species over the Ag₄²⁺ cluster in a zeolite is investigated. The results of the reaction route mapping for H₂ + O₂ reveal that OH and OOH species are formed over the Ag₄²⁺ cluster via an activation barrier lower than that of OH formation from H₂O dissociation. Then, reaction route mapping is performed to examine the reactivity of the OH and OOH species with NO molecules over the Ag₄²⁺ cluster, resulting in the facile reaction path of HONO formation. With the aid of the automated reaction route mapping, the promotion effect of H₂ addition on the SCR reaction was computationally proposed (boosting the formation of OH and OOH species). In addition, the present study emphasizes that automated reaction route mapping is a powerful tool to elucidate the complicated reaction pathway on multi-nuclear clusters.

Structural dynamics of Ru clusters during nitrogen dissociation in ammonia synthesis

The dynamic evolution of catalyst structures greatly influences the reactivity, especially sub-nanometer clusters, exhibiting complex configurational fluctuation. In the present work, we study the structural dynamics of a Ru₁₉ cluster during the dissociation of N₂ and calculate the reaction free energies using ab initio molecular dynamics (AIMD). Our AIMD calculation predicts a peak-shaped reaction entropy curve due to the adsorption-induced phase transition of the Ru₁₉ cluster. The low melting points of sub-nanometer clusters make it possible to activate N₂ at low temperatures. This work demonstrates that the dynamic changes of cluster structures have a non-negligible effect on reaction free energy and offer an opportunity for achieving ammonia synthesis under mild conditions.

Size-dependent phase transitions boost catalytic activity of sub-nanometer gold clusters

The characterization and identification of the dynamics of cluster catalysis are crucial to unraveling the origin of catalytic activity. However, the dynamical catalytic effects during the reaction process remain unclear. Herein, we investigate the dynamic coupling effect of elementary reactions with the structural fluctuations of sub-nanometer Au clusters with different sizes using ab initio molecular dynamics and the free energy calculation method. It was found that the adsorption-induced solid-to-liquid phase transitions of the cluster catalysts give rise to abnormal entropy increase, facilitating the proceeding of reaction, and this phase transition catalysis exists in a range of clusters with different sizes. Moreover, clusters with different sizes show different transition temperatures, resulting in a non-trivial size effect. These results unveil the dynamic effect of catalysts and help understand cluster catalysis to design better catalysts rationally.

Structural Characterization of Nickel-Doped Aluminum Oxide Cations by Cryogenic Ion Trap Vibrational Spectroscopy

Isolated nickel-doped aluminum oxide cations (NiO_m)(Al₂O₃)_n(AlO)⁺ with m = 1-2 and n = 1-3 are investigated by infrared photodissociation (IRPD) spectroscopy in combination with density functional theory and the single-component artificial force-induced reaction method. IRPD spectra of the corresponding He-tagged cations are reported in the 400-1200 cm^-1 spectral range and assigned based on a comparison to calculated harmonic IR spectra of low-energy isomers. Simulated spectra of the lowest energy structures generally match the experimental spectra, but multiple isomers may contribute to the spectra of the m = 2 series. The identified structures of the oxides (m = 1) correspond to inserting a Ni-O moiety into an Al-O bond of the corresponding (Al₂O₃)_1-3(AlO)⁺ cluster, yielding either a doubly or triply coordinated Ni²⁺ center. The m = 2 clusters prefer similar structures in which the additional O atom either is incorporated into a peroxide unit, leaving the oxidation state of the Ni²⁺ atom unchanged, or forms a biradical comprising a terminal oxygen radical anion Al-O^•- and a Ni³⁺ species. These clusters represent model systems for under-coordinated Ni sites in alumina-supported Ni catalysts and should prove helpful in disentangling the mechanism of selective oxidative dehydrogenation of alkanes by Ni-doped catalysts.

Generative adversarial networks for transition state geometry prediction

This work introduces a novel application of generative adversarial networks (GANs) for the prediction of starting geometries in transition state (TS) searches based on the geometries of reactants and products. The multi-dimensional potential energy space of a chemical reaction often complicates the location of a starting TS geometry, leading to the correct TS combining reactants and products in question. The proposed TS-GAN efficiently maps the space between reactants and products and generates reliable TS guess geometries, and it can be easily combined with any quantum chemical software package performing geometry optimizations. The TS-GAN was trained and applied to generate TS guess structures for typical chemical reactions, such as hydrogen migration, isomerization, and transition metal-catalyzed reactions. The performance of the TS-GAN was directly compared to that of classical approaches, proving its high accuracy and efficiency. The current TS-GAN can be extended to any dataset that contains sufficient chemical reactions for training. The software is freely available for training, experimentation, and prediction at https://github.com/ekraka/TS-GAN.

Combined Automated Reaction Pathway Searches and Sparse Modeling Analysis for Catalytic Properties of Lowest Energy Twins of Cu13

In nanocatalysis, growing attention has recently been given to investigation of energetically low-lying structural isomers of atomic clusters, because some isomers can demonstrate better catalytic activity than the most stable structures. In this study, we present a comparative investigation of catalytic activity for NO dissociation of a pair of the energetically degenerated isomers of Cu₁₃ cluster having C₂ and C _s symmetries. It is shown that although these isomers have similar structural, electronic, and optical properties, they can possess very different catalytic activities. The effect of isomerization between cluster isomers is considered using state-of-the-art automated reaction pathway search techniques such as an artificial force induced reaction (AFIR) method as a part of a global reaction route mapping (GRRM) strategy. This method allows effectively to locate a large number of possible reaction pathways and transition states (TSs). In total, 12 TSs for NO dissociation were obtained for Cu₁₃, of C₂, C _s, as well as I _h isomers. Sparse modeling analysis shows that LUMO is strongly negatively correlated with total energy of TSs. For most TSs, LUMO has the antibonding character of NO, consisting of the interaction between π* of NO and SOMO of Cu₁₃. Therefore, an increase in the strength of interaction between NO molecule and Cu₁₃ cluster causes the rise in energy of the LUMO, resulting in lowering of the TS energy for NO dissociation. The combination of the automated reaction pathway search technique and sparse modeling represents a powerful tool for analysis and prediction of the physicochemical properties of atomic clusters, especially in the regime of structural fluxionality, where traditional methods based on random geometry search analyses are difficult.

Understanding CO oxidation on the Pt(111) surface based on a reaction route network

Kinetic analysis by the rate constant matrix contraction on the reaction route network of CO oxidation on the Pt(111) surface obtained by the artificial force induced reaction reveals the impact of entropic contributions arising from a variety of local minima and transition states.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.

Excess charge driven dissociative hydrogen adsorption on Ti2O4−

The mechanism of dissociative D₂ adsorption on Ti₂O₄⁻ is studied using infrared photodissociation spectroscopy in combination with density functional theory calculations.