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Sana Bougueroua

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5 records found

Journal article (2026) - Alexander A. Kolganov, Sana Bougueroua, Marie Pierre Gaigeot, Matthew P. Conley, Evgeny A. Pidko
Capturing the dynamic behavior of active sites on complex, amorphous supports is a significant challenge in modeling single-site catalysts, particularly in surface organometallic catalysts. These systems are characterized by a well-defined chemical bonding pattern that coexists with the fluxionality of ancillary ligands and the inherent complexity of the support. Here, we present a conceptual workflow that integrates reactive molecular dynamics with advanced graph theory-based analysis to systematically explore the configurational space of supported catalysts. First, we used enhanced molecular dynamics to overcome local energy barriers and generate a diverse ensemble of structures. Then, we applied graph-based algorithms to distinguish truly distinct isomers from mere conformers and rotamers. Applying this approach to the model system of 1,1′-bis(n-butyl-cyclopentadienyl) zirconium dihydride on a dehydrated amorphous silica model, our method reveals the significant role of local silica strain in shaping the ensemble of active site configurations: catalysts grafted on silanol groups with strained confinement exhibit a diverse array of reaction pathways and significant energy stabilization, whereas less-strained environments yield a more restricted set of accessible configurations. This work demonstrates that combining molecular dynamics with graph theory provides an intuitive framework for unraveling the complex, fluxional behavior of supported catalysts. ...
Journal article (2025) - V.J. Lagerweij, Sana Bougueroua, P. Habibi, P. Dey, Marie Pierre Gaigeot, O. Moultos, T.J.H. Vlugt
Accurate conductivity predictions of KOH(aq) are crucial for electrolysis applications. OH– is transferred in water by the Grotthuss transfer mechanism, thereby increasing its mobility compared to that of other ions. Classical and ab initio molecular dynamics struggle to capture this enhanced mobility due to limitations in computational costs or in capturing chemical reactions. Most studies to date have provided only qualitative descriptions of the structure during Grotthuss transfer, without quantitative results for the transfer rate and the resulting transport properties. Here, machine learning molecular dynamics is used to investigate 50,000 transfer events. Analysis confirmed earlier works that Grotthuss transfer requires a reduction in accepted and a slight increase in donated hydrogen bonds to the hydroxide, indicating that hydrogen-bond rearrangements are rate-limiting. The computed self-diffusion coefficients and electrical conductivities are consistent with experiments for a wide temperature range, outperforming classical interatomic force fields and earlier AIMD simulations. ...
Journal article (2024) - Sana Bougueroua, A.A. Kolganov, Chloe Helain, Coralie Zens, Dominique Barth, E.A. Pidko, Marie Pierre Gaigeot
Some of our recent developments and applications of algorithmic graph theory for extracting the physical and chemical properties of materials from molecular dynamics simulations are presented. From the chemical viewpoint, the power of graph theory is illustrated in the search for a catalyst's active sites at a silica solid surface. From the physical viewpoint, we present graph algorithms that recognize the structural motifs that exist at the silica/liquid water interface. Statistical analyses of the instances of these surface–water motifs provide a detailed understanding of the structures and dynamics at the aqueous interface. ...

High-Throughput Reactivity Exploration for Extended Databases of Transition-Metal Catalysts

Journal article (2023) - Ali Hashemi, Sana Bougueroua, Marie Pierre Gaigeot, Evgeny A. Pidko
A method is introduced for the automated analysis of reactivity exploration for extended in silico databases of transition-metal catalysts. The proposed workflow is designed to tackle two key challenges for bias-free mechanistic explorations on large databases of catalysts: (1) automated exploration of the chemical space around each catalyst with unique structural and chemical features and (2) automated analysis of the resulting large chemical data sets. To address these challenges, we have extended the application of our previously developed ReNeGate method for bias-free reactivity exploration and implemented an automated analysis procedure to identify the classes of reactivity patterns within specific catalyst groups. Our procedure applied to an extended series of representative Mn(I) pincer complexes revealed correlations between structural and reactive features, pointing to new channels for catalyst transformation under the reaction conditions. Such an automated high-throughput virtual screening of systematically generated hypothetical catalyst data sets opens new opportunities for the design of high-performance catalysts as well as an accelerated method for expert bias-free high-throughput in silico reactivity exploration. ...

A Reaction Network Graph-Theoretical Tool for Automated Mechanistic Studies in Computational Homogeneous Catalysis

Journal article (2022) - Ali Hashemi, Sana Bougueroua, Marie Pierre Gaigeot, Evgeny A. Pidko
Exploration of the chemical reaction space of chemical transformations in multicomponent mixtures is one of the main challenges in contemporary computational chemistry. To remove expert bias from mechanistic studies and to discover new chemistries, an automated graph-theoretical methodology is proposed, which puts forward a network formalism of homogeneous catalysis reactions and utilizes a network analysis tool for mechanistic studies. The method can be used for analyzing trajectories with single and multiple catalytic species and can provide unique conformers of catalysts including multinuclear catalyst clusters along with other catalytic mixture components. The presented three-step approach has the integrated ability to handle multicomponent catalytic systems of arbitrary complexity (mixtures of reactants, catalyst precursors, ligands, additives, and solvents). It is not limited to predefined chemical rules, does not require prealignment of reaction mixture components consistent with a reaction coordinate, and is not agnostic to the chemical nature of transformations. Conformer exploration, reactive event identification, and reaction network analysis are the main steps taken for identifying the pathways in catalytic systems given the starting precatalytic reaction mixture as the input. Such a methodology allows us to efficiently explore catalytic systems in realistic conditions for either previously observed or completely unknown reactive events in the context of a network representing different intermediates. Our workflow for the catalytic reaction space exploration exclusively focuses on the identification of thermodynamically feasible conversion channels, representative of the (secondary) catalyst deactivation or inhibition paths, which are usually most difficult to anticipate based solely on expert chemical knowledge. Thus, the expert bias is sought to be removed at all steps, and the chemical intuition is limited to the choice of the thermodynamic constraint imposed by the applicable experimental conditions in terms of threshold energy values for allowed transformations. The capabilities of the proposed methodology have been tested by exploring the reactivity of Mn complexes relevant for catalytic hydrogenation chemistry to verify previously postulated activation mechanisms and unravel unexpected reaction channels relevant to rare deactivation events. ...