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An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology

Tautomerism induces bending and twisting of biogenic crystals

Understanding and exploiting material flexibility through phenomena such as the bending and twisting of molecular crystals has been a subject of increased interest owing to the number of applications that benefit from these properties, such as optoelectronics, mechanophotonics, soft robotics, and smart sensors. Here, we report the growth of spontaneously bent and twisted ammonium urate crystals induced by the keto–enol tautomerism of the urate molecule. The major tautomer is native to biogenic crystals, whereas the minor tautomer functions as an effective crystal growth modifier to induce naturally bent and twisted ammonium urate crystals. We show that the degree of curvature can be tailored based on the judicious selection of growth conditions. A combination of state-of-the-art microscopy and spectroscopy techniques are used to characterize the origin of bending. Spatially resolved nano-electron diffraction and high-resolution electron microscopy of naturally bent crystals show nearly single crystallinity with local lattice deformations generated by a combination of screw and edge dislocations. These observations are consistent with photoinduced force microscopy and contact resonance atomic force microscopy, which confirmed spatially resolved changes in the intermolecular interactions and the mechanical properties throughout the cross-sectional and axial regions of bent crystals. A mechanism of bending involving the generation of regionally specific dislocations is proposed as an alternative to more commonly reported models. These findings highlight a unique characteristic of tautomeric crystals that may have broader implications for other biogenic materials.

Science & Technology - Other Topics

Predicting Atomistic Transitions with Transformers

Accurate knowledge of the atomistic transition pathways in materials and material surfaces is crucial for many material science problems. However, conventional simulation techniques used to find these transitions are extremely computationally intensive. Even with large-scale, accelerated material simulations, the computational cost constrains the applicable domain in practice. Machine learning models, with the potential to learn the complex emergent behaviors governing atomistic transitions as a fast surrogate model, have great promise to predict transitions with a vastly reduced computational cost. Here, we demonstrate how transformers can be trained to predict atomistic transitions in nano-clusters. We show how we evaluate physical validity of the predictions and how a multitude of additional, different microstates can be generated by slightly varying the data provided to the model.

36 MATERIALS SCIENCE

Dynamic nanodomains dictate macroscopic properties in lead halide perovskites

Lead halide perovskites have emerged as promising materials for solar energy conversion and X-ray detection owing to their remarkable optoelectronic properties. However, the microscopic origins of their superior performance remain unclear. Here we show that low-symmetry dynamic nanodomains present in the high-symmetry average cubic phases, whose characteristics are dictated by the A-site cation, govern the macroscopic behaviour. We combine X-ray diffuse scattering, inelastic neutron spectroscopy, hyperspectral photoluminescence microscopy and machine-learning-assisted molecular dynamics simulations to directly correlate local nanoscale dynamics with macroscopic optoelectronic response. Our approach reveals that methylammonium-based perovskites form densely packed, anisotropic dynamic nanodomains with out-of-phase octahedral tilting, whereas formamidinium-based systems develop sparse, isotropic, spherical nanodomains with in-phase tilting, even when crystallography reveals cubic symmetry on average. We demonstrate that these sparsely distributed isotropic nanodomains present in formamidinium-based systems reduce electronic dynamic disorder, resulting in a beneficial optoelectronic response, thereby enhancing the performance of formamidinium-based lead halide perovskite devices. By elucidating the influence of the A-site cation on local dynamic nanodomains, and consequently, on the macroscopic properties, we propose leveraging this relationship to engineer the optoelectronic response of these materials, propelling further advancements in perovskite-based photovoltaics, optoelectronics and X-ray imaging.

Materials Science

Effect of Preparation Conditions of Fe@SiO2 Catalyst on Its Structure Using High-Pressure Activity Studies in a 3D-Printed SS Microreactor

Fischer–Tropsch synthesis (FTS) in a 3D-printed stainless steel (SS) microchannel microreactor was investigated using Fe@SiO2 catalysts. The catalysts were prepared by two different techniques: one pot (OP) and autoclave (AC). The mesoporous structure of the two catalysts, Fe@SiO2 (OP) and Fe@SiO2 (AC), ensured a large contact area between the reactants and the catalyst. They were characterized by N2 physisorption, H2 temperature-programmed reduction (H2-TPR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron microscopy (XPS), and thermogravimetric analysis–differential scanning calorimetry (TGA-DSC) techniques. The AC catalyst had a clear core–shell structure and showed a much greater surface area than that prepared by the OP method. The activities of the catalysts in terms of FTS were studied in the 200–350 °C temperature range at 20-bar pressure with a H2/CO molar ratio of 2:1. The Fe@SiO2 (AC) catalyst showed higher selectivity and higher CO conversion to olefins than Fe@SiO2 (OP). Stability studies of both catalysts were carried out for 30 h at 320 °C at 20 bar with a feed gas molar ratio of 2:1. The Fe@SiO2 (AC) catalyst showed higher stability and yielded consistent CO conversion compared to the Fe@SiO2 (OP) catalyst.

Biochemistry & Molecular Biology

Identification of potent inhibitors of JUN N-terminal kinases for treatment of endometriosis and associated pain

Endometriosis, defined as the ectopic growth of endometrial tissue outside of the uterine cavity, is an inflammatory and hormone-dependent disease that causes excruciating pelvic pain, infertility, and significantly decreases quality of life in affected patients. The JUN N-terminal kinases (JNKs) are a leading class of nonhormonal therapeutic targets that have been validated in preclinical models of endometriosis and in a Phase 1/2 clinical trial. Despite their therapeutic potential, JNK inhibitors with increased potency and specificity are needed to address the inflammatory pathology of endometriosis and to prevent disease progression. Leveraging a DNA-encoded chemical library collection of ~4 billion compounds, we identified lead inhibitor CDD-2428 and optimized derivatives, CDD-2728 and CDD-3013, with excellent binding affinity to JNK1-3 (K d = 0.12 to 3.7 nM), enhanced selectivity, metabolic stability, and cellular permeability. Crystallographic and biochemical studies confirmed that CDD-3013 exhibited superior kinase selectivity with improved efficacy compared to existing JNK inhibitors. In primary endometriosis cell models, CDD-2728 and CDD-3013 suppressed JNK-dependent inflammatory signaling, dampening pathways linked to pain, invasion, angiogenesis, and macrophage recruitment. In an endometriosis mouse model, both CDD-2728 and CDD-3013 reduced endometriotic lesion size, macrophage infiltration, and cellular proliferation, showing in vivo efficacy. When tested in a lipopolysaccharide-induced hyperalgesia model, CDD-2728 and CDD-3013 decreased markers of induced pain, as measured by changes in a dynamic weight bearing test and Grimace scores. These findings nominate CDD-2728 and CDD-3013 as potent, nonhormonal therapeutic candidates for endometriosis with broad anti-inflammatory and analgesic activity, addressing a critical unmet clinical need.

Madasu, Chandrashekhar [Department of Pathology an

Mechanisms of Alkali Ionic Transport in Amorphous Oxyhalides Solid State Conductors

Amorphous oxyhalides have attracted significant attention due to their relatively high ionic conductivity (1 mS cm –1 ), excellent chemical stability, mechanical softness, and facile synthesis routes via standard solid‐state reactions. These materials exhibit an ionic conductivity that is almost independent of the underlying chemistry, in stark contrast to what occurs in crystalline conductors. In this work, we employ machine learning interatomic potentials to construct large‐scale molecular dynamics trajectories encompassing hundreds of nanoseconds to obtain statistically converged transport properties. We find that the amorphous state consists of chain fragments of metal‐anion tetrahedra of various lengths. By analyzing the residence time of alkali cations migrating around tetrahedrally‐coordinated metals, we find that oxygen anions limit alkali diffusion. By computing the full Einstein expression of the ionic conductivity, we demonstrate that the alkali transference number of these materials is strongly influenced by distinct‐particles correlations, while alkali transport is dictated by uncorrelated self‐diffusion. By extending this analysis to chemical compositions AMX 2.5 O 0.75 , spanning different alkaline (A = Li, Na, K), metallic (M = Al, Ga, In), and halogen (X = Cl, Br, I) species, we clarify why the diffusion properties of these materials remain largely insensitive to variations in atomic isovalent chemistry.

amorphous materials

Effect of Fe on Co-Based SiO2Al2O3 Mixed Support Catalyst for Fischer–Tropsch Synthesis in 3D-Printed SS Microchannel Microreactor

This research explores the effect of a composite support of SiO2 and Al2O3 with Fe and Co incorporated as catalysts for Fischer–Tropsch synthesis (FTS) using a 3D-printed stainless steel (SS) microchannel microreactor. Two mesoporous catalysts, FeCo/SiO2Al2O3 and Co/SiO2Al2O3, were synthesized via a one-pot (OP) method and extensively characterized using N2 physisorption, XRD, SEM, TEM, H2-TPR, TGA-DSC, FTIR, and XPS. H2-TPR results revealed that the synthesis method significantly affected the reducibility of metal oxides, thereby influencing the formation of active FTS sites. SEM-EDS and TEM further revealed a well-defined hexagonal matrix with a porous surface morphology and uniform metal ion distribution. FTS reactions, carried out in the 200–350 °C temperature range at 20 bar with a H2/CO molar ratio of 2:1, exhibited the highest activity for FeCo/SiO2Al2O3, with up to 80% CO conversion. Long-term stability was evaluated by monitoring the catalyst performance for 30 h on stream at 320 °C under identical reaction conditions. The catalyst was initially active for the methanation reaction for up to 15 h, after which the selectivity for CH4 declined. Correspondingly, the C4+ selectivity increased after 15 h of time-on-stream, indicating a shift in the product distribution toward longer-chain hydrocarbons. This trend suggests that the catalyst undergoes gradual activation or restructuring under reaction conditions, which enhances chain growth over time. The increase in C4+ products may be attributed to the stabilization of the active sites and suppression of methane or light hydrocarbon formation.

Biochemistry & Molecular Biology

Analytical Model for Atomic Relaxation in Twisted Moiré Materials

By virtue of being atomically thin, the electronic properties of heterostructures built from two-dimensional materials are strongly influenced by atomic relaxation. The atomic layers behave as flexible membranes rather than rigid crystals. Here we develop an analytical theory of lattice relaxation in twisted moiré materials. We obtain analytical results for the lattice displacements and corresponding pseudo gauge fields, as a function of twist angle. We benchmark our results for twisted bilayer graphene and twisted WSe 2 bilayers using large-scale molecular dynamics simulations. Our single-parameter theory is valid in graphene bilayers for twist angles 𝜃 ≳ 0.7°, and in twisted WSe 2 for 𝜃 ≳ 1.6°. Furthermore, we also investigate how relaxation alters the electronic structure in twisted bilayer graphene, providing a simple extension to the continuum model to account for lattice relaxation.

36 MATERIALS SCIENCE

Acute Exposure to Aerosolized Nanoplastics Modulates Redox-Linked Immune Responses in Human Airway Epithelium

Micro- and nanoplastics (MPs and NPs) are pervasive environmental pollutants detected in aquatic ecosystems, with emerging evidence suggesting their presence in airborne particles generated by water body motion. Inhalation exposure to airborne MPs and NPs remains understudied despite documented links between occupational exposure to these particles and adverse respiratory outcomes, including airway inflammation, oxidative stress, and chronic respiratory diseases. This study explored the effects of acute NP exposure on a fully differentiated 3D human airway epithelial model derived from 14 healthy donors. Airway epithelium was exposed to aerosolized 50 nm polystyrene NPs at concentrations ranging from 2.5 to 2500 µg/mL for three minutes per day over three days. Functional assays revealed no significant alterations in tissue integrity, cell survival, mucociliary clearance, or cilia beat frequency, suggesting intact epithelial function post-exposure. However, cytokine and chemokine profiling identified a significant five-fold increase in CCL3 (MIP-1α), a neutrophilic chemoattractant, in NP-exposed samples compared to controls. This was corroborated by increased neutrophil chemotaxis in response to conditioned media from NP-exposed tissues, indicating a pro-inflammatory neutrophilic response. Conversely, levels of interleukins (IL-21, IL-2, IL-15), CXCL10, and TGF-β were significantly reduced, suggesting immunomodulatory effects that may impair adaptive immune responses and tissue repair mechanisms. These findings demonstrate that short-term exposure to NP-containing aerosols induces a distinct pro-inflammatory response in airway epithelium, characterized by enhanced neutrophil recruitment and reduced secretion of key immune modulators. These findings underscore the potential for aerosolized NPs to induce oxidative and inflammatory stress, raising concerns about their long-term impact on respiratory health and redox regulation.

Biochemistry & Molecular Biology

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern

Hydrogen diffusion induced dislocation transformations in a nickel superalloy

The diffusion of hydrogen in metals and alloys induces embrittlement that can adversely affect the structural properties. We examine the adsorption and diffusion of hydrogen in Inconel-718 (IN-718), and scrutinize the ensuing effects on the dislocation behavior in the alloy to elucidate the fundamental mechanisms of hydrogen-microstructure interactions from classical molecular simulations. Hydrogen adsorption increases with time until the surface saturates, while hydrogen diffusion exhibits strong temperature dependence, with diffusion coefficients converging above 1300 K regardless of the initial hydrogen concentration in the alloy. The diffusion in IN-718 is significantly sluggish than in pure Ni, Fe, or Cr, and is strongly impacted by hydrogen concentrations, resulting in an order of magnitude higher diffusion coefficient for hydrogen (10-14 m2/s relative to 10-15 m2/s) at high concentrations, especially below 600 K. Hydrogen diffusion coefficient varies from 10-12 to 10-15 m2/s in IN-718 depending on temperature (500–1400 K). More critically, our results reveal that increasing hydrogen concentration induces microstructural changes in the alloy, transforming perfect dislocations into stair-rods and Shockley partials, with higher temperatures favoring the latter. The results are significant for hydrogen fuel applications to gain insights into the materials chemistry for designing safer and more efficient propulsion systems, particularly in high-performance environments related to controlled hydrogen combustion applications.

Banerjee, Tanumoy

Internally Catalyzed Hydrogen Atom Transfer (I-CHAT)—A New Class of Reactions in Combustion Chemistry

The current paradigm of low-T combustion and autoignition of hydrocarbons is based on the sequential two-step oxygenation of fuel radicals. The key chain-branching occurs when the second oxygenation adduct (OOQOOH) is isomerized releasing an OH radical and a key ketohydroperoxide (KHP) intermediate. The subsequent homolytic dissociation of relatively weak O–O bonds in KHP generates two more radicals in the oxidation chain leading to ignition. Based on the recently introduced intramolecular “catalytic hydrogen atom transfer” mechanism (J. Phys. Chem. 2024, 128, 2169), abbreviated here as I-CHAT, we have identified a novel unimolecular decomposition channel for KHPs to form their classical isomers—enol hydroperoxides (EHP). The uncertainty in the contribution of enols is typically due to the high computed barriers for conventional (“direct”) keto–enol tautomerization. Remarkably, the I-CHAT dramatically reduces such barriers. The novel mechanism can be regarded as an intramolecular version of the intermolecular relay transfer of H-atoms mediated by an external molecule following the general classification of such processes (Catal. Rev.-Sci. Eng. 2014, 56, 403). Here, we present a detailed mechanistic and kinetic analysis of the I-CHAT-facilitated pathways applied to n-hexane, n-heptane, and n-pentane models as prototype molecules for gasoline, diesel, and hybrid rocket fuels. We particularly examined the formation kinetics and subsequent dissociation of the γ-enol-hydroperoxide isomer of the most abundant pentane-derived isomer γ-C5-KHP observed experimentally. To gain molecular-level insight into the I-CHAT catalysis, we have also explored the role of the internal catalyst moieties using truncated models. All applied models demonstrated a significant reduction in the isomerization barriers, primarily due to the decreased ring strain in transition states. In addition, the longer-range and sequential H-migration processes were also identified and illustrated via a combined double keto–enol conversion of heptane-2,6-diketo-4-hydroperoxide as a potential chain-branching model. To assess the possible impact of the I-CHAT channels on global fuel combustion characteristics, we performed a detailed kinetic analysis of the isomerization and decomposition of γ-C5-KHP comparing I-CHAT with key alternative reactions—direct dissociation and Korcek channels. Calculated rate parameters were implemented into a modified version of the n-pentane kinetic model developed earlier using RMG automated model generation tools (ACS Omega, 2023, 8, 4908). Simulations of ignition delay times revealed the significant effect of the new pathways, suggesting an important role of the I-CHAT pathways in the low-T combustion of large alkanes.

Biochemistry & Molecular Biology

Discrete Rotational Energy for Polyatomic Molecules in Direct Simulation Monte Carlo

The environments experienced by vehicles upon entry into planetary atmospheres generally result in severe aerothermodynamic loading. These flows are characterized by the formation of strong shock waves, behind which high temperatures and non-equilibrium environments are generated, and the accurate prediction of internal energy relaxation and chemical kinetics becomes important. This manuscript focuses on the internal relaxation of the rotational energy of polyatomic molecules. Previous work has described the implementation of a discrete rotational energy model for diatomic molecules (linear rotators). Later, Gimelshein et. al extended this model to include polyatomic molecular internal energies. However, they did not include details on how to generate the particles at equilibrium conditions and centrifugal distortion was not included in their model. The purpose of the present study is to extend the afore-mentioned models to the treatment of discrete rotational energy in polyatomic molecules with the addition of centrifugal distortion. An overview of the background theory needed for the implementation of the model will be given followed by the model itself and verification of the model. For example, sampled versus Boltzmann distributions are compared in Figure 1 for CH3 (oblate rotator – two quantum numbers) and examples of thermal relaxation behavior for linear and non-linear rotators are presented in Figure 2. In addition, comparisons of thermophysical properties will be presented, as well as examples of adiabatic relaxation and application to hypersonic flow.

Rarefied Gas Dynamics

The Contaminant Footprint of Landed Spacecraft: Toward an Inventory and Modelling Framework

All spacecraft generate and carry contaminants, i.e., unwanted and potentially harmful material. When a spacecraft lands and operates in near-vacuum, as onto Earth’s Moon, it introduces contaminants into its environment that may compromise mission science objectives and engineering performance. Contamination of solar system bodies may irrevocably degrade targets of unique value to planetary scientists, for instance, as lunar landed spacecraft introduce propellant effluents into the otherwise pristine ice of the Moon’s permanently shadowed regions. NASA’s planetary protection discipline seeks to ensure that solar system bodies are not contaminated, for scientific purposes, by terrestrial material (i.e., forward contamination). This interest aligns with planetary science interest in mitigating the transport of terrestrial contaminants onto solar system bodies and in controlling types of contamination that could compromise the scientific value of samples or measurements. NASA, and other entities that practice planetary science, have compelling and multidisciplinary interests in the preservation of special regions and sampling sites of high scientific value – including lunar permanently shadowed regions (PSRs) – from inadvertent contamination by any spacecraft, and in understanding the contamination of such regions by all spacecraft. Organic molecular contamination here represents a primary threat. Organic molecules will be introduced to solar system bodies by nominal landed spacecraft and crew processes – including by the action of descent and ascent engines; natural materials outgassing; and crew environmental and life support system sources. Molecular contaminants can also travel in the free-molecular sense at global scale across near-vacuum bodies, including into regions where they may be permanently trapped. This presentation will address a high-level study to identify sources of contaminants – in particular, organic material – generated by landed spacecraft along with the transport vectors by which these contaminants can reach sites of scientific interest on bodies like the Moon. A vision for an integrated modeling framework for the organic contamination footprint of spacecraft missions, individually and collectively, will also be described and presented along with initial conclusions related to organic molecular transport.

Gas Dynamics

Cyclic Peptides for Lanthanide Binding

Lanthanide ions are difficult to separate from one another due to their similar chemical properties. The discovery of lanthanide-binding peptides and proteins in nature has led to an increased interest in the possibility of utilizing the strong binding of peptides to lanthanide ions for their separations; as such, there has been an effort to identify or design peptides with improved lanthanide binding and selectivity toward particular lanthanide ions. Here, in this study, we designed and characterized lanthanide-binding cyclic peptides (LBCPs) with molecular dynamics simulations, electronic structure calculations, and emission spectroscopy. Luminescent decay measurements were done to determine the number of water molecules coordinated to the Eu 3+ ion in Eu-LBCP complexes and compare to the predicted number of water molecules by computation to assess the lanthanide-binding affinity of LBCPs. Measured stability constants show binding of the LBCPs to the Eu 3+ ion with stronger than micromolar affinity. We were able to identify multiple peptides that selectively bind to middle lanthanides. We describe the structural basis of the lanthanide-binding selectivity trend with strongest binding to the middle lanthanides, followed by the heavier lanthanides, and finally to the lighter ions.

ions

Development of large-scale, 3D Printed high temperature ceramic material

Through this collaborative effort, a new 3D printing platform for ceramics called laser-induced slip casting (LIS) was explored and developed for improving the processing and manufacture of silicon carbide (SiC), a high temperature ceramic material. This method prints layers of ceramic slips/slurries with subsequent selective-laser heating to dry each layer to build a 3D structure. The completed and dried part is then sintered. This manufacturing process is inherently lower cost than alternative ceramic printing methods such as binder jet technology or stereolithography when it comes to the feedstock material but is more expensive than robocasting or direct ink writing. However, it has the potential to make more controlled parts with less defects compared to robocasting. The largest cost is the heating source for the printer. With this technique, there is potential to make large ceramic parts in a near-net shape. Further, there is no known commercial manufacturing of 3D printed ceramics that creates a large range of different high-density ceramics at large scale. The goals and outcomes for the development of the new printing technology were: 1) assessing the technology with alumina by characterizing coupons, 2) printing and sintering of silicon carbide (SiC), and 3) characterization and properties testing of materials printed and a scale-up of SiC part(s). Through this collaborative project, it was sought to provide the best solution to achieving highly dense and near-net shaped ceramic parts at large scale and reduced cost. The goal was to produce high density sintered materials for applications in defense, energy generating systems, armor, and wear parts using 3D printing methods. Variables including powder particle sizes, dispersant molecular weights (MWs), binders, printing parameters, and post processing were explored as well as the characterization of the physical properties (add specifics here).

36 MATERIALS SCIENCE

Revealing the Hidden Third Dimension of Point Defects in Two-Dimensional MXenes

Point defects govern many important functional properties of two-dimensional (2D) materials. However, resolving the three-dimensional (3D) arrangement of these defects in multi-layer 2D materials remains a fundamental challenge, hindering rational defect engineering. Here, we overcome this limitation using an artificial intelligence-guided electron microscopy workflow to map the 3D topology and clustering of atomic vacancies in Ti3C2TX MXene. Our approach reconstructs the 3D coordinates of vacancies across hundreds of thousands of lattice sites, generating robust statistical insight into their distribution that can be correlated with specific synthesis pathways. This large-scale data enables us to classify a hierarchy of defect structures-from isolated vacancies to nanopores-revealing their preferred formation and interaction mechanisms, as corroborated by molecular dynamics simulations. This work provides a generalizable framework for understanding and ultimately controlling point defects across large volumes, paving the way for the rational design of defect-engineered functional 2D materials.

2D materials