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An Integrated Study of Pd(0)-Halide Interactions in Pd Oxidative Addition to Organic Halides: Uncovering the “Super Iodine” Character of Pd(0)
No full textPd(0) oxidative addition (OA) to organic halides is a fundamental step in many catalytic organic transformations. Previous mechanistic studies have shown that the electronic/steric nature of ligand, metal coordination unsaturation, halide identity and the presence of an additive all have sizable influences on reaction reactivity and selectivity. A single parameter-based rational design fully integrating all important factors in a quantitative manner remains elusive, due to the complex nature of Pd(0) OA. To address this challenge, a study of Pd(0)-halide interactions which are crucial for the 3-centered concerted mechanism, is initiated in this work by integrating the key progress in organometallic chemistry and the relatively well-established halogen bonding knowledge, mimicking the “data-driven” method. The achieved advanced understanding of the mechanisms in this work includes five key parts: 1) uncovering the “super iodine” character of Pd(0), 2) uncovering the bonding nature of Pd-halide (organic halide) interaction and its essential role in Pd(organic halide) precomplex before OA; 3) a molecular mechanism for the additive effect, and a theoretical prediction of a halogen transfer pathway for OA to specific organic halides; 4) demystifying the known super reactivity of the ligand-controlled Pd catalysis with inactive aryl chlorides; and ultimately 5) proposing a proof-of-concept of surface molecule electrostatic potential-based rational design of OA
SynPlanner: an end-to-end tool for synthesis planning
No full textSynPlanner is an open-source tool for retrosynthetic planning, designed to increase flexibility in training and developing customized retrosynthetic planning solutions from raw chemical data. It integrates Monte Carlo Tree Search (MCTS) with graph neural networks to evaluate applicable reaction rules (policy network) and the synthesizability of intermediate products (value network). SynPlanner can be used directly with pre-trained policy/value networks or fine-tuned on custom data through an automated end-to-end training pipeline. Additionally, SynPlanner enables the training of custom value functions on discovered synthesis routes to improve predictive performance. The tool includes original modules for atom-to-atom mapping, reaction curation, standardization, and extraction of reaction rules, ensuring the reproducibility of the training pipeline from initial data to trained retro-synthetic models. SynPlanner is available on GitHub at https://github.com/Laboratoire-de-Chemoinformatique/SynPlanne
Inverse Design of Singlet Fission Materials with Uncertainty-Controlled Genetic Optimization
No full textSinglet fission has shown potential for boosting the power conversion efficiency of solar cells, but the scarcity of suitable molecular materials hinders its implementation. We introduce an uncertainty-controlled genetic algorithm (ucGA) based on ensemble machine learning predictions from different molecular representations that concurrently optimizes excited state energies, synthesizability, and singlet exciton size for the discovery of singlet fission materials. The ucGA allows us to efficiently explore the chemical space spanned by the reFORMED fragment database, which consists of 45,000 cores and 5,000 substituents derived from crystallographic structures assembled in the FORMED repository. Running the ucGA in an exploitative setup performs local optimization on variations of known singlet fission scaffolds, such as acenes. In an explorative mode, hitherto unknown candidates displaying excellent excited state properties for singlet fission are generated. We suggest a class of heteroatom-rich mesoionic compounds as acceptors for charge-transfer mediated singlet fission. When included in larger conjugated donor-acceptor systems, these units exhibit strong localization of the triplet state, favorable diradicaloid character and suitable triplet energies for exciton injection into semiconductor solar cells. As the proposed candidates are composed of fragments from synthesized molecules, they are likely synthetically accessible
AdsMT: A multi-modal transformer for predicting global minimum adsorption energy
No full textThe fast assessment of the global minimum adsorption energy (GMAE) between catalyst surfaces and adsorbates is crucial for large-scale catalyst screening. However, multiple adsorption sites and numerous possible adsorption configurations for each surface/adsorbate combination make it prohibitively expensive to calculate the GMAE through density functional theory (DFT). Thus, we designed a novel multi-modal transformer called AdsMT to rapidly predict the GMAE based on surface graphs and adsorbate feature vectors without any site-binding information. The AdsMT model effectively captures the intricate relationships between adsorbates and surface atoms through the cross-attention mechanism, hence avoiding the enumeration of adsorption configurations. Three diverse benchmark datasets were constructed, opening new avenues for further research on the challenging GMAE prediction task. Our AdsMT framework demonstrates excellent performance by adopting the tailored graph encoder and transfer learning, achieving mean absolute errors of 0.09, 0.14, and 0.39 eV, respectively. Beyond GMAE prediction, AdsMT\u27s cross-attention scores showcase the interpretable potential to identify the most energetically favorable adsorption sites. Additionally, uncertainty quantification was integrated into our models to enhance the trustworthiness of the predictions. While primarily focused on heterogeneous catalyst screening, our multi-modal approach has potential applications across materials science and chemistry
Deciphering the Stacking Language of Honeycomb Bilayer Materials: A Comprehensive Review of Groups 13 to 15
No full textResearch into two-dimensional materials and their stacking configurations has experienced a considerable upswing in recent years. Experimental and theoretical exploration of various forms of stacking has revealed unexpected phenomena. However, one of the significant challenges in the study of layered structures is the nomenclature used in the literature, which is sometimes ambiguous, makes comparison between different systems difficult, and can inadvertently lead to the omission of specific stackings. This review addresses the need for a unified framework for understanding and categorizing the stacking arrangements of bilayer honeycomb materials consisting of elements from Groups 13 to 15. We used a uniform ABC notation to standardize the nomenclature and facilitate comparative literature analysis, but also examine their limitations and emphasise the need for JAM notation
Bulky phosphine ligands promote palladium-catalysed protodeboronation
No full textThe Suzuki-Miyaura cross-coupling reaction is plagued by protodeboronation, an undesirable side reaction with water that consumes the boronic acid derivatives required for the cross-coupling reaction. Meticulous mechanistic studies have previously established protodeboronation to be highly sensitive to the nature of the boronic reagent and reaction conditions. Particularly, the presence of bases, which are essential for the Suzuki-Miyaura coupling, is known to catalyse protodeboronation. However, protodeboronation catalysed by palladium-phosphine complexes, the benchmark catalyst system for Suzuki-Miyaura cross-coupling, has been largely overlooked. We demonstrate, using automated high-throughput experimentation, comprehensive computational mechanistic analyses and kinetic modelling, that protodeboronation is accelerated by palladium(II) complexes bound to bulky phosphine ligands. While sterically hindered ligands are typically used to facilitate difficult cross-couplings, these ligands can instead paradoxically impede cross-coupling product formation, requiring careful and judicious consideration when choosing ligands for Suzuki-Miyaura cross-couplings
The spatial distribution of lipophilic cations in gradient copolymers regulates pDNA binding interactions, polyplex aggregation, and transgene expression
No full textSynthetic polymers—chemically versatile and affordable materials—are promising nanocarriers for the intracellular delivery of nucleic acids. Copolymers comprising of lipophilic cations and neutral hydrophilic co-monomers effectively complex and deliver bulky nucleic acid payloads such as plasmids (pDNA). In this work, we demonstrate that the spatial distribution of lipophilic cations governs the complexation pathways, serum stability, and biological performance of polymer–pDNA complexes (polyplexes). Hitherto, investigators focused predominantly on block and statistical copolymers while largely ignoring gradient copolymers, where the density of lipophilic cations diminishes (gradually or steeply) along polymer backbones. Our goal is to engineer gradient copolymers that combine the colloidal stability of polyplexes formed from block copolymers with the high transfection efficacy of statistical copolymers. We synthesized length- and compositionally-equivalent gradient copolymers (G1–G3) via reversible addition fragmentation chain transfer polymerization in addition to equivalent statistical (S) and block (B) copolymers. We mapped microstructure-dependent differences in pDNA loading per polyplex, pDNA conformational changes, and polymer–pDNA binding thermodynamics via static light scattering, circular dichroism spectroscopy, and isothermal titration calorimetry, respectively. B exhibited vastly different pDNA complexation profiles from the other four copolymers while loading the most pDNA per polyplex. Further, we discovered that subtle modulation of gradient steepness effectively negotiates trade-offs among pDNA delivery efficiency, cytotoxicity, and colloidal stability in serum. For instance, G1 overcame the colloidal instability of S polyplexes in serum, while maintaining comparable transfection efficiency and cell viability. Microstructural contrasts did not elicit differences in complement activation but governed polycation-triggered hemolysis. Our work demonstrates that the spatial distribution of lipophilic cations is an effective, albeit underutilized, design handle to improve polyplex physical properties and pDNA delivery capacity
From Methane to Methanol: Pd-iC-CeO2 Catalysts Engineered for High Selectivity via Mechano-Chemical Synthesis
No full textIn the pursuit of selective conversion of methane directly to methanol in the liquid-phase, a common challenge is the concurrent formation of undesirable liquid oxygenates or combustion byproducts. However, we demonstrate that monometallic Pd-CeO2 catalysts, modified by carbon, created by a simple mechanochemical synthesis method exhibit 100% selectivity towards methanol at 75°C, using hydrogen peroxide as oxidizing agent. The solvent free synthesis yields a distinctive Pd-iC-CeO2 interface, where interfacial carbon (iC) modulates metal-oxide interactions and facilitates tandem methane activation and peroxide decomposition, thus resulting in an exclusive methanol selectivity of 100% with a rate of 117 µmol/gcat at 75°C. Notably, solvent interactions of H2O2 (aq) were found to be critical for methanol selectivity through a DFT-simulated Eley-Rideal-like mechanism. This mechanism uniquely enables the direct conversion of methane into methanol via a solid-liquid-gas process
[ECCE]-Coordinated (E = P, As) Ruthenium Complexes in Different Oxidation States: Ru(I) (E = P), Ru(II) (E = P, As) and Ru(III) (E = As)
No full textTargeting Ru(III) and Ru(I) η2-alkyne complexes, 2,2’-(iPr2E)2-substituted diphenylacetylenes (1-E, E = P, As) were employed for the prepara-tion of [ECCE]-coordinated Ru(II) complexes, which were examined with respect to 1e− oxidation and reduction. Starting from [(η6-cymene)RuCl2]2 and 1-E, ligand cyclization reactions (via attack of one iPr2E moiety at the alkyne) were observed and found to afford cyclic aryl ylidic mesoionic carbenes (2-E). Attempts to ring-open these complexes were unsuccessful for E = P, but found to proceed smoothly for E = As, which led to the isolation of cis-[AsCCAs]RuCl2(MeCN) (3-As). To also gain access to the corresponding [PCCP]-coordinated derivative (3-P), the reactions between 1-E (E = P, As) and cis-(MeCN)2(COD)RuCl2 ∙ 2 MeCN were examined, which led to the envisioned complexes 3-E for E = As and E = P. Compounds cis-[ECCE]RuCl2(MeCN) (3-E) and their carbonyl derivatives cis-[ECCE]RuCl2(CO) (5-E) were oxidized using PhICl2, which led to an oxidative dichlorination of the alkyne in the case of 5-E. The latter dichlorination was found to occur trans-selective to afford complexes of the type [trans-E(Cl)C=C(Cl)E]RuCl2(CO) (6-E), while unselective oxidation processes set in upon treatment of 3-E with PhICl2. Although the envisioned Ru(III) complexes [ECCE]RuCl3 (7-E) were detectable for E = P and E = As, only the arsa-derivative 7-As was obtained in a pure form, namely via oxidation of cis-[ECCE]RuCl2(THT) (8), which is accessible for E = As only. Upon reduction of compounds 3-E, a hitherto unprecedented Ru(I) η2-alkyne complex, [PCCP]RuCl (9), was obtained for E = P, while multi-ple attempts to also isolate the corresponding arsa-derivative met with failure. The former square planar Ru(I) complex (9) was characterized comprehensibly and examined in detail by means of DFT and CASSCF calculation. Upon treatment of 9 with TlPF6, a diamagnetic µ-Tl-bridged compound (10) with a nearly linear Ru−Tl−Ru array was formed and isolated in high yields. Careful analysis of the bonding situation suggested that the Ru−Tl−Ru moiety in 10 is best interpreted in terms of a 3c-4e− bond
Local and Global Structural Effects of Doping on Ionic Conductivity in Na3SbS4 Solid Electrolyte
No full textAmong Na-ion solid electrolytes, Na3SbS4 has achieved high ionic conductivity (s_ion) exceeding 10 mS/cm through aliovalent doping. s_ion enhancement due to aliovalent doping is qualitatively explained by the increase in the concentration of defects that mediate ion diffusion. However, a rigorous atomic-scale mechanistic explanation is needed. Doping also affects s_ion by modifying ion mobility - an effect that is not well understood and often overlooked. We use first-principles defect calculations to mechanistically explain and quantify the increase/decrease in Na vacancy concentration due to aliovalent doping of Na3SbS4. By focusing on isovalent doping, we reveal local and global structural effects of doping on the migration barrier, and therefore, ion mobility. In conjunction with experiments, we demonstrate the interplay between the local and global effects. Doping with heavier anions to achieve more polarizable frameworks is a common approach to enhancing s_ion. Our findings present a unique approach to enhancing s_ion by doping with smaller and lighter cations that form stiffer bonds with anions, which in turn soften the parent framework