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At least 55 records · Page 3

Synthesis and Characterization of Methacrylamide-Based Block Random Copolymers via Amine Functionalization of Polystyrene- Block -Poly(Pentafluorophenyl Methacrylate) Toward Enhanced Amenability to Manufacturing Criteria in Nanolithography

Recent interest in manipulating the chemistry of block copolymers (BCPs) to manage the covarying properties necessary to meet manufacturing criteria in nanolithography has resulted in the development and expansion of the A-block-(B-random-C) BCP architecture, where the random block allows for the decoupling of thermodynamic and wetting properties. Previous reports of such BCPs have used click chemistry to create the desired random block, but all such instances possess additional functional groups that are susceptible to undesirable side reactions upon annealing, such as cross-linking and surface grafting. This study reports the substitution reaction of polystyrene-block-poly(pentafluorophenyl methacrylate) (PS-b-PPFMA) with primary amines. The resulting methacrylamide structure of the functionalized random block has only an amide linkage between the attached functional group and the polymer backbone, thereby omitting any sources of side reactions within the BCP. The outcomes of this report also demonstrate the enhanced thermal stability of these materials by virtue of their stable amide bonds. A range of random copolymer compositions is assessed to develop BCPs in which the random block has approximately the same surface energy as the PS block. These BCPs can self-assemble into perpendicular lamellae and are therefore promising candidates for directed self-assembly.

block copolymers↗

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗

AEcroscopy: A Software–Hardware Framework Empowering Microscopy Toward Automated and Autonomous Experimentation

Microscopy has been pivotal in improving the understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most characterization labs. However, traditional microscopy operations are still limited largely by a human-centric click-and-go paradigm utilizing vendor-provided software, which limits the scope, utility, efficiency, effectiveness, and at times reproducibility of microscopy experiments. Here, in this work, a coupled software–hardware platform is developed that consists of a software package termed AEcroscopy (short for Automated Experiments in Microscopy), along with a field-programmable-gate-array device with LabView-built customized acquisition scripts, which overcome these limitations and provide the necessary abstractions toward full automation of microscopy platforms. The platform works across multiple vendor devices on scanning probe microscopes and electron microscopes. It enables customized scan trajectories, processing functions that can be triggered locally or remotely on processing servers, user-defined excitation waveforms, standardization of data models, and completely seamless operation through simple Python commands to enable a plethora of microscopy experiments to be performed in a reproducible, automated manner. This platform can be readily coupled with existing machine-learning libraries and simulations, to provide automated decision-making and active theory-experiment optimization to turn microscopes from characterization tools to instruments capable of autonomous model refinement and physics discovery.

47 OTHER INSTRUMENTATION↗

INSPIRED: Inelastic neutron scattering prediction for instantaneous results and experimental design

Inelastic neutron scattering (INS) has unique advantages in probing how atoms vibrate and how the vibrations propagate and interact. Such dynamic information is crucial in understanding various material properties, from heat capacity, thermal conductivity, phase transitions, and chemical reactions to more exotic quantum behavior. The analysis and interpretation of the INS spectra often start from a model structure of the sample, followed by a series of calculations to obtain the simulated spectra to compare with experiments. The conventional way to perform such calculations usually requires significant time, computing resources, and specialized expertise. Here, we present a new program named INSPIRED (Inelastic Neutron Scattering Prediction for Instantaneous Results and Experimental Design), which enables users to perform rapid INS simulations in several different ways on their personal computers in just a few clicks, with the crystal structure as the only input file. Specifically, the users can choose a pre-trained symmetry-aware neural network (coupled with an autoencoder) to predict the phonon density of states (DOS), 1D S(E) and 2D S(|Q|,E) spectra for any given structure. One can also choose an existing density functional theory (DFT) calculation from a database (containing over 12,000 crystals), and quickly obtain the simulated INS spectra for single crystals and powders. It is also possible to use pre-trained universal machine learning force fields to relax a given crystal structure, calculate the phonon dispersion and DOS, and, subsequently, the INS spectra. All these functions are implemented with a PyQt graphic user interface. Finally, we expect these new tools will benefit broad user communities and significantly improve the efficiency of experiment design, execution, and data analysis for INS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

From PROTAC to inhibitor: Structure-guided discovery of potent and orally bioavailable BET inhibitors

An X-ray structure of a CLICK chemistry-based BET PROTAC bound to BRD2(BD2) inspired synthesis of JQ1 derived heterocyclic amides. This effort led to the discovery of potent BET inhibitors displaying overall improved profiles when compared to JQ1 and birabresib. A thiadiazole derived 1q (SJ1461) displayed excellent BRD4 and BRD2 affinity and high potency in the panel of acute leukaemia and medulloblastoma cell lines. A structure of 1q co-crystalised with BRD4-BD1 revealed polar interactions with the AZ/BC loops, in particular with Asn140 and Tyr139, rationalising the observed affinity improvements. In addition, exploration of pharmacokinetic properties of this class of compounds suggest that the heterocyclic amide moiety improves drug-like features. Finally, our study led to the discovery of potent and orally bioavailable BET inhibitor 1q (SJ1461) as a promising candidate for further development.

60 APPLIED LIFE SCIENCES↗

Thermodynamics, local structure, and transport of protons in triple-conducing oxide, BaCo 0.4 Fe 0.4 Zr 0.1 Y 0.1 O 3-δ (BCFZY4411)

Triple-conducting oxides (TCOs) are an emerging class of mixed ionic and electronically conducting materials that show great promise for oxygen reduction/oxygen evolution (ORR/OER) electrocatalysis—primarily in high-temperature ceramic electrochemical cells— but also in aqueous alkaline environments. Their high activity is attributed, at least in part, to their ability to incorporate and transport three mobile charge carriers: protons, oxygen vacancies, and electron-holes Despite their promise, fundamental studies of TCOs are challenging, as transport dynamics from three charge carriers cannot be fully disentangled via traditional electrical measurement techniques. Characterizing proton dynamics in TCOs is particularly difficult as protons are generally the minority carrier, and their conduction response is typically obscured by the oxygen vacancies and electron holes. Here, we demonstrate successful isolation of the proton behavior in an archetypal TCO, BaCo 0.4 Fe 0.4 Zr 0.1 Y 0.1 O 3-δ (BCFZY4411), using a combination of non-electrical techniques. We determine proton uptake and oxygen non-stoichiometry (δ) using thermogravimetric analysis (TGA). X-ray absorption near edge structure (XANES) and neutron diffraction (ND) are used to validate the oxidation state of Co and the δ values obtained through TGA. We apply 1H solid-state magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) to provide insights into local structure, dynamics, and proton kinetics. Finally, the proton transport properties are further quantified using tracer isotope exchange with time-of-flight secondary ion mass spectrometry (ToF-SIMS). Despite the very low proton concentrations in BCFZY4411 (<0.2% under most conditions), our analysis suggests that the oxygen Manuscript File Click here to view linked References 2 reduction and evolution reactions are nevertheless limited by the oxygen ion kinetics (e.g., oxygen surface exchange) rather than the proton kinetics at the reduced operating temperatures (<500 °C) that are targeted for electrochemical cell applications. These findings provide a comprehensive understanding of proton behavior in BCFZY4411 and pave the way for advancing the fundamental study of TCOs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Wetting Behavior of A -block- (B- random -C) Copolymers with Equal Block Surface Energies on Surfaces Functionalized with B- random -C Copolymers

To form nanopatterns with self-assembled block copolymers (BCPs), it is desirable to have through-film domains that are oriented perpendicular to the substrate. The domain orientation is determined by the interfacial interactions of the BCP domains with the substrate and with the free surface. Here, we use thin films of two different sets of BCPs with A-block-(B-random-C) architecture matched with a corresponding B-random-C copolymer nanocoating on the substrate to demonstrate two distinct wetting behaviors. The two sets of A-b-(B-r-C) BCPs are made by using thiol–epoxy click chemistry to functionalize polystyrene-block-poly(glycidyl methacrylate) with trifluoroethanethiol (TFET) and either 2-mercaptopyridine (2MP) or methyl thioglycolate (MTG). For each set of BCPs, the composition ratio of the two thiols in the BCP (φ 1 ) is found that results in the two blocks of the modified BCP having equal surface energies (Δγ air = 0). The corresponding B-r-C random copolymers were synthesized and used to modify the substrate, and the composition ratio (φ 2 ) values that resulted in the two blocks of the BCP having equal interfacial energy with the substrate (Δγ sub = 0) were determined with scanning electron microscopy. The correlation between each block’s γ sub value and the interaction parameter, χ, is employed to explain the different wetting behaviors of the two sets of BCPs. For the thiol pair 2MP and TFET, the values of φ 1 and φ 2 that lead to Δγ air = 0 and Δγ sub = 0, respectively, are significantly different. A similar difference was observed between the φ 1 and φ 2 values that lead to Δγ air = 0 and Δγ sub = 0 for the BCPs made with the thiol pair MTG and TFET. In the latter case, for Δγ sub = 0 two windows of φ 2 are identified, which can be explained by the thermodynamic interactions of the specific thiol pair and the A-b-(B-r-C) architecture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Physical and Chemical Responses of Amidine-Containing Polymers in the Capture and Release of CO 2

Polymeric materials containing amidine motifs are of high interest due to their ability to reversibly capture and release CO 2 at ambient temperature. Here, in this study, we probe physical and chemical responses of styrene-based copolymers containing linear amidine motifs as functions of CO 2 and inert gas exposures and temperature. A copper-catalyzed azide–alkyne cycloaddition “click” reaction involving N′-propargyl-N,N-dimethylacetamidine is used to modify random copolymers, resulting in an array of linear amidine motifs along the chain backbone with the amount of CO 2 -active amidine controlled by the copolymer composition. Through thermogravimetric measurements, we demonstrate that the amidine-functionalized copolymers efficiently capture CO 2 upon exposure to a stream of CO 2 (at 27 °C) and release it at a slightly elevated temperature (50 °C) when exposed to an inert gas stream (N 2 ). In addition to displaying a maximum adsorption capacity of 22 wt % in the presence of pure CO 2 , the copolymers show composition-dependent direct air capture (DAC) behaviors. Small molecule analogs are used to definitively understand degradation via chemical hydrolysis of the amidine moiety, which leads to insolubility and a large reduction in CO 2 adsorption capacity (1.7 wt %). Neutron vibrational spectroscopy and DFT calculations confirm that CO 2 binds strongly to the amidine motif, inducing a strong bending of the CO 2 molecule from its linear geometry. The coupled insights into mechanisms and behaviors of CO 2 adsorption in amidine-functionalized polymers provides a foundation for future investigations of CO 2 -responsive polymers and soft materials to improve carbon capture and sequestration technologies.

Chun, Danielle J.↗

Incorporation of Thioacetate Pendants on a Polyalkenamer Enables High Extensibility

This study focuses on functionalizing polycyclooctene (PCOE) with thioacetate groups using thiol–ene click chemistry. The ethylene thioacetate (EVSA) copolymers produced vary in thioacetate incorporation (4–25 mol %) via a controlled semibatch addition technique with AIBN dosing. Copolymers with 4–14 mol % thioacetate are semicrystalline, while those with 20–25 mol % are amorphous. Increased functionalization correlates with decreased crystallinity and increased stretchability, with the highest functionalization (25 mol %) showing a modulus of 0.045 MPa and 2000% elongation at break. Here, this behavior is due to the pseudoprecise functionalization of the thioacetate pendants and intrinsic cross-linking that occurs during melt processing. Broadband dielectric spectroscopy (BDS) indicates a low activation energy barrier (16 kJ/mol for the β process), suggesting potential self-healing applications.

36 MATERIALS SCIENCE↗

Post-Modification of Crystalline Peptoid Nanomembranes with Active Nanoparticles for Efficient Photooxidation of a Mustard Gas Simulant

Peptoids (or poly-N-substituted glycines) hold immense potential for assembling into hierarchically structured functional materials via controlled molecular interactions. To create self-assembled materials with tailored functionalities, peptoid sequences are often conjugated with reactive or recognition motifs to enable applications including specific binding, biomimetic catalysis, and fluorescence imaging. However, the direct integration of bulky functional motifs into peptoid sequences can disrupt assembly processes and structural outcomes. Herein, we present a post-modification strategy for functionalizing pre-formed 2D crystalline assemblies. Through introducing clickable active sites, such as azide, alkyne, or thiol groups into a peptoid sequence, site-specific conjugation is achieved post-assembly via efficient “click”-type reactions. This strategy enables the ordered alignment of functional groups and gold nanoparticles (Au NPs) on the surface of 2D peptoid nanomaterials with controlled density, while preserving their high crystallinity and structural integrity. Furthermore, we demonstrated that nanomembranes functionalized with both Au NPs and porphyrins enhance the efficiency and selectivity of the photooxidation of 2-chloroethyl ethyl sulfide, a simulant of sulfur mustard. This innovative strategy lays the groundwork for advancing peptoid-based functional materials across diverse applications, from catalysis to biomedicine.

Chemistry↗

Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies

Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Forster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with posttranscriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions. However, due to the bulky sizes of functional groups or labeling probes used, such strategies might cause structural perturbation and decrease the accuracy of distance measurements. Here, we synthesize an a-thiophosphorylated variant of rTPT3TP (rTPT3aS), which allows for post-transcriptional site-specific labeling of large RNAs at the internal a-phosphate backbone via maleimide-modified probes. Subsequent PELDOR, XSI, and smFRET measurements result in narrower distance distributions than labeling at the TPT3 base. The presented strategy provides a new route to empower the molecular rulers for structural and dynamic studies of large RNA and its complex.

59 BASIC BIOLOGICAL SCIENCES↗

Kinetic Analysis of Proton-Coupled Electron Transfer at an Electrode-Immobilized Complex

An alkyne-terminated cobalt complex, [Co(Cp)(dppe ≡H )(Cl)] + (Cp = cyclopentadienyl; dppe ≡H = 1,2-bis-(di-(4-ethynyl-phenyl)phosphino)ethane), (Co ≡H ) was immobilized onto a glassy carbon electrode using two attachment strategies: Cu(I) catalyzed azide–alkyne click chemistry and reductive electropolymerization. The modified electrodes prepared through reductive electropolymerization exhibit current densities and peak resolutions for the electrochemical reduction of the cobalt species, which are amenable to electroanalytical quantification of coupled chemical reactions. Through peak shift analysis of cyclic voltammograms recorded in the presence of 4-chloroanilinium tetrafluoroborate, we quantified the proton transfer rate constant for the stepwise proton-coupled electron transfer reaction that reduces the electrode-immobilized [Co(Cp)(dppe ≡H )(Cl)] + to [H–Co(Cp)(dppe ≡H )] + (k PT app = (9.3 ± 1.8) × 10 5 M –1 s –1 ). In conclusion, the extraction of kinetic parameters for an elementary proton-coupled electron transfer reaction of an electrode-immobilized complex represents the first experimental measurement of its type and lays crucial groundwork for kinetic analyses of hybrid catalyst–electrode architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Viscosity-Controlled Thiol–Ene Reaction and Its Impact on Mechanical Response of Dynamic Networks

The impact of curing conditions on the final properties of thioester-thiol-based dynamic polymer networks was systematically investigated. Despite identical monomer and cross-linker compositions, networks synthesized in the absence of solvent exhibited significantly higher shear moduli and longer relaxation times compared to those cured in solvent. These differences arise from viscosity-controlled photoinitiated thiol–ene reactions, where reduced chain mobility under solvent-free conditions suppresses termination between two polymer radicals, leading to higher reaction conversion. Fourier Transform Infrared (FTIR) spectroscopy and solid-state NMR (ssNMR) spectroscopy confirmed a greater degree of “click” reaction completion in higher viscosity environments. Control experiments revealed that prolonged radical lifetimes and suppressed termination reactions under solvent-free curing conditions contribute to these variations. Here, this study highlights the crucial role of processing conditions in determining cross-link density and, consequently, the dynamic mechanical behavior of polymer networks. It demonstrates that, beyond polymer chemistry, dynamic cross-linker design, and phase separation, curing conditions serve as a key design parameter for tailoring material performance to specific applications.

polymers↗

Tunable and Degradable Dynamic Thermosets from Compatibilized Polyhydroxyalkanoate Blends

Polyhydroxyalkanoates (PHAs) are versatile, biobased polyesters that are often targeted for use as degradable thermoplastic replacements for polyolefins. Given the substantial chemical diversity of PHA, their potential as cross-linked polymers could also enable similar platforms for reversible, degradable thermosets. In this work, we genetically engineered Pseudomonas putida KT2440 to synthesize poly(3-hydroxybutyrate-co-3-hydroxyundecenoate) (PHBU), which contains both 3-hydroxybutyrate and unsaturated 3-hydroxyundecenoate components. To reduce the brittleness of this polymer, we physically blended PHBU with the soft copolymer poly(3-hydroxydecanonate-co-3-hydroxyundecenoate) in mass ratios of 1:3, 1:1, and 3:1. Upon observing varying degrees of immiscibility by scanning electron microscopy, we installed dynamic boronic ester cross-links via thiol–ene click chemistry, which resulted in compatibilized dynamic thermoset blends ranging in hard, medium, and soft rubber or elastomer thermomechanical profiles. These dynamic thermoset blends were subjected to controlled biological degradation experiments in freshwater conditions, achieving timely mass loss despite the cross-linked architectures. Overall, this work highlights a two-component platform for the production of degradable and reprocessable dynamic thermoset blends suitable for several classes of cross-linked polymer technologies from tailored, biological PHA copolymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Solid-State Side-Chain Functionalization of Conjugated Polymers for Expanded Chemical and Functional Versatility

Conjugated polymers that integrate diverse chemical functionalities with high electronic performance are essential for advanced organic electronic, optoelectronic, and biointerfaced technologies. Achieving such multifunctionality typically requires grafting functional units onto polymer side chains. However, conventional solution-phase approaches remain constrained by solubility limitations, side-chain-induced packing disruptions, and challenges in preserving charge transport. Here, we introduce a solid-state side-chain functionalization strategy that exploits a swellable polar side-chain architecture and azide–alkyne click chemistry to enable efficient molecular diffusion and reaction throughout predeposited polymer thin films. This approach substantially broadens the chemical compatibility of graftable units and mitigates the adverse effects on the electrical property. Moreover, the method supports spatially selective functionalization within a continuous film, enabling the patterned incorporation of chemically distinct groups to produce spatially defined optical properties. Here, this solid-state strategy thus provides a versatile platform for constructing conjugated polymers with expanded chemical versatility, preserved electronic performance, and programmable spatial functionality.

Conjugated polymers↗

Hierarchical Chiral Self-Assembly of Nanocylinders Composed of Sequence-Defined Mesogenic Dimers

Chiral ensembles can arise through supramolecular curvature that resolves geometric frustrations in the packing of bent, achiral molecular or colloidal building blocks. Here, we leverage orthogonal protection−deprotection click chemistry to create sequence-defined mesogenic heterodimers exhibiting emergent chirality. We compare the hierarchical self-assembly of the synthesized asymmetric, achiral heterodimers, which differ only in the position of a methyl substituent. Both dimers form chiral spherulites composed of nanocylinders. However, the detailed arrangement of nanocylinders depends on the position of the methyl substituent and the crystallization conditions. Despite the chemical similarity, in one dimer, two crystalline forms are optically active. They form conglomerates of dextrorotatory and levorotatory spherulites. The other dimer forms more highly anisotropic spherulites that mask circular birefringence arising from the misorientation of nanocylinders, while mapping of nanocylinder directors reveals a sense at the spherulite surface. We propose that differences in nanocylinder arrangements may arise from changes in nanocylinder curvature and dimensions dictated by the methyl substituent position, inducing chirality. These results demonstrate multiscale hierarchical assembly relevant to dense systems of tubular structures and highlight the role of sequence and molecular design in directing the bottom-up hierarchical self-assembly and chirality of mesogenic systems.

Alkyls↗

Yi Liu answers questions about 15 years of research on covalent organic frameworks

The article is an interview with Dr. Yi Liu. Dr. Liu is the facility director at the Molecular Foundry, Lawrence Berkeley National Laboratory. Trained as a supramolecular chemist and after a postdoctoral stay and working on click chemistry in Sharpless’s group he started his independent research career working on organic electronics, porous materials, and covalent organic frameworks (COFs). His aim is to develop nanostructured electronic materials through the design, synthesis and manipulation of tailor-made molecular constituents. He answers questions about research on covalent organic frameworks.

36 MATERIALS SCIENCE↗

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Abstract Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis , here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗