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DOE OSTI2025

Modulating Poly(oligocyclobutane) Properties Through Backbone Modifications

Poly(1,n′-divinyl)oligocyclobutane (pDVOCB) has emerged as a class of poly(cycloolefin) that is amenable to chemical recycling and demonstrates promising thermomechanical properties. However, their high melting temperatures coupled with insolubility makes melt processing challenging due to thermo-oxidation of internal alkenes. To address these issues, we describe a series of polymers incorporating modifications to the pDVOCB backbone and analyze the effects on material stability and processability. Intentional migration of the internal 1,2-disubstituted alkenes to an exocyclic trisubstituted position yields isomerized pDVOCB (IpDVOCB) which exhibits a depression of thermal transitions by up to 50 °C. Conversely, elimination of stereoirregularity between enchained DVOCB oligomers through alkene saturation yields hydrogenated pDVOCB (HpDVOCB), resulting in elevated thermal transitions by up to 30 °C. Furthermore, these shifts are attributed to changes in crystal defect density which is strongly influenced by chain stereoregularity. Understanding these behaviors guides future polymer design and expands the control and use of this new class of recyclable poly(cycloolefin)s.

Differential scanning calorimetry↗

DOE OSTI2023

Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates

As genetic code expansion advances beyond l-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-l-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi–Dunitz angle of 76–115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Harnessing Aromatic‐Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification

Abstract Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high‐resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor‐1, which is targeted by osteoporosis drugs. These results should motivate other structure‐based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Harnessing Aromatic‐Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification

36 MATERIALS SCIENCE↗

DOE OSTI2022

Engineering stability, longevity, and miscibility of microtubule-based active fluids

Microtubule-based active matter provides insight into the self-organization of motile interacting constituents. In this work, we describe several formulations of microtubule-based 3D active isotropic fluids. Dynamics of these fluids is powered by three types of kinesin motors: a processive motor, a non-processive motor, and a motor which is permanently linked to a microtubule backbone. Another modification uses a specific microtubule crosslinker to induce bundle formation instead of a non-specific polymer depletant. In comparison to the already established system, each formulation exhibits distinct properties. These developments reveal the temporal stability of microtubule-based active fluids while extending their reach and the applicability.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Detailed Method for the Purification of Rhamnogalacturonan-I (RG-I) in Arabidopsis thaliana

The plant cell wall is a dynamic and complex extracellular matrix that not only provides structural integrity and determines cell shape but also mediates intercellular communication. Among its major components, pectins play essential roles in cell adhesion, wall porosity, hydration, and flexibility. Rhamnogalacturonan-I (RG-I), a structurally diverse pectic polysaccharide, remains one of the least understood components of the plant cell wall. Its backbone is substituted with arabinan, galactan, and arabinogalactan side chains that vary in length, branching, and composition across tissues, species, and developmental stages. In addition, RG-I can undergo modifications such as backbone acetylation, further contributing to its structural complexity and functional diversity. To advance understanding of RG-I, we present a detailed method for isolating RG-I from the model plant Arabidopsis thaliana . Leveraging Arabidopsis as a model system provides major advantages owing to its well-characterized genome and powerful molecular toolkit, enabling deeper investigation into the roles of RG-I in plant development and responses to environmental stress. Our method consists of two major steps: an initial chemical extraction using oxalate, followed by endo-polygalacturonase (EPG) digestion to fragment the pectic domains. An advantage of this approach is that it produces a dry material that can be stored at room temperature without special handling and does not introduce chemicals that may interfere with downstream analyses. The purified RG-I can be used for detailed compositional and structural analyses, as well as for functional studies of enzymes involved in pectin biosynthesis, modification, and degradation. Although this protocol was developed for isolating RG-I from Arabidopsis rosette leaves, it is also applicable to other Arabidopsis organs and other plant species.

25 ENERGY STORAGE↗

DOE OSTI2026

Improved Protein Semi-Synthesis Enables Biophysical Studies of Thioamide Destabilization of β-Sheet Interactions

Abstract Thioamides are natural post-translational modifications of the peptide backbone and can be introduced synthetically to probe protein folding or functionalize peptides for translational applications. In this work, we demonstrate that thioamide-containing peptides with C-terminal thioesters can be efficiently generated using Knorr pyrazole activation and used in subsequent native chemical ligation reactions to generate thioamide-containing proteins. We compare this method to acyl azide activation and find that both routes provide similar yields. We also investigate ultrasound-mediated desulfurization of the ligation site cysteine for potential advantages over chemical radical initiators. Scaling up our syntheses allows us to study thioamide perturbations to the β-sheet region of the B1 domain of protein G (GB1) as well as β-strand interactions in amyloid fibrils of the Parkinson’s disease protein α-synuclein. In both contexts, we observe dramatic destabilization of the β-sheet networks, manifested in decreased GB1 thermal stability and altered folding and slowed aggregation of α-synuclein. These findings illustrate the impact that a single atom substitution can have on cooperative hydrogen-bonding networks and prompt future study of both systems.

Yanagawa, Evan S. K. [University of Pennsylvania ,↗

DOE OSTI2020

Disruption of a key ligand-H-bond network drives dissociative properties in vamorolone for Duchenne muscular dystrophy treatment

Duchenne muscular dystrophy is a genetic disorder that shows chronic and progressive damage to skeletal and cardiac muscle leading to premature death. Antiinflammatory corticosteroids targeting the glucocorticoid receptor (GR) are the current standard of care but drive adverse side effects such as deleterious bone loss. Through subtle modification to a steroidal backbone, a recently developed drug, vamorolone, appears to preserve beneficial efficacy but with significantly reduced side effects. We use combined structural, biophysical, and biochemical approaches to show that loss of a receptor-ligand hydrogen bond drives these remarkable therapeutic effects. Moreover, vamorolone uniformly weakens coactivator associations but not corepressor associations, implicating partial agonism as the main driver of its dissociative properties. Additionally, we identify a critical and evolutionarily conserved intramolecular network connecting the ligand to the coregulator binding surface. Interruption of this allosteric network by vamorolone selectively reduces GR-driven transactivation while leaving transrepression intact. Our results establish a mechanistic understanding of how vamorolone reduces side effects, guiding the future design of partial agonists as selective GR modulators with an improved therapeutic index.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Tuning the Mobility of Indacenodithiophene-Based Conjugated Polymers via Coplanar Backbone Engineering

Conjugated polymers based on indacenodithiophene-benzothiadiazole (IDT-BT) have attracted great interest due to their high charge carrier mobilities while being low crystallinity (i.e. near-amorphous.) They represent a promising design strategy to achieve both excellent stretchability and electrical performance. Here, we describe an approach on structural modifications of IDT-BT, namely by introducing non-covalent interactions and substituting building blocks to promote extended coplanar backbones. We systematically investigated the effects of structural modifications on backbone conformation, polymer aggregations, and charge carrier mobilities. Among the investigated polymers, the fluorinated derivative IDT-FBT demonstrated the highest charge carrier mobility of 5.19 cm 2 /Vs, along with low activation energy and Urbach energy indicating its low energy disorder level. The high mobility was attributed to the higher backbone planarity reinforced by S···F and H···F non-covalent interactions and improved interchain interactions through strong aggregation. In conclusion, our findings indicate that increasing backbone coplanarity may further improve mobility in low crystallinity conjugated polymers.

36 MATERIALS SCIENCE↗

DOE OSTI2025

The pectin puzzle: Decoding the fine structure of rhamnogalacturonan-I (RG-I) in Arabidopsis thaliana uncovers new pectin features

Pectin is generally divided into four distinct structural categories, namely homogalacturonan, xylogalacturonan, rhamnogalacturonan I (RG-I) and rhamnogalacturonan II. While much of the structural diversity of homogalacturonan, xylogalacturonan and rhamnogalacturonan II has been elucidated, the structural features of RG-I are less well understood. In this work, we employed multiple complementary analytical techniques to present a detailed structural analysis of RG-I in the model species Arabidopsis thaliana . Starting with highly purified RG-I from different Arabidopsis tissues, we employed comparative linkage and nuclear magnetic resonance analysis along with mass spectrometry analysis of enzymatically digested RG-I oligosaccharides. Besides the presence of the canonical α-1,5-arabinan, β-1,4-galactan, β-1,6-galactan and arabinogalactan RG-I side chains of varying lengths, we show that a large portion of the β-1,6-galactan is terminated by either 4-O-methyl β-glucuronic acid (GlcA) residues or, to a smaller degree, β-GlcA that lacks the Me-ether group. Importantly, O-acetylation of RG-I GalA residues is a minor modification while 10 % of the backbone Rha residues are 3-O-acetylated, and most of the acetylated Rha is additionally branched with β-galactose substituents. Taken together, the combined results of these different analytical techniques present the most comprehensive structural overview of Arabidopsis thaliana RG-I to date.

25 ENERGY STORAGE↗

DOE OSTI2024

Artificial Intelligence Transforming Post-Translational Modification Research

Post-Translational Modifications (PTMs) are covalent changes to amino acids that occur after protein synthesis, including covalent modifications on side chains and peptide backbones. Many PTMs profoundly impact cellular and molecular functions and structures, and their significance extends to evolutionary studies as well. In light of these implications, we have explored how artificial intelligence (AI) can be utilized in researching PTMs. Initially, rationales for adopting AI and its advantages in understanding the functions of PTMs are discussed. Then, various deep learning architectures and programs, including recent applications of language models, for predicting PTM sites on proteins and the regulatory functions of these PTMs are compared. Finally, our high-throughput PTM-data-generation pipeline, which formats data suitably for AI training and predictions is described. We hope this review illuminates areas where future AI models on PTMs can be improved, thereby contributing to the field of PTM bioengineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Scalable Frontal Oligomerization: Insights from Advanced Mass Analysis

Linear oligomers of dicyclopentadiene (DCPD) are reactive precursors for thermoplastic and thermoset materials. Unlike the foul-smelling parent monomer, oligomers composed of DCPD are odorless. With appropriate modification of the end-group or backbone chemistry, telechelic DCPD oligomers have potential utility as cross-linkers and as macromonomer precursors for block and graft copolymers. Most existing methods to produce oligo-DCPD, however, require solvent, are relatively slow, and necessitate air-free techniques. Here we show that frontal ring-opening metathesis oligomerization (FROMO) of neat DCPD and other norbornene derivatives rapidly generates hundreds of grams of material in minutes with catalyst loadings of 0.5 mM. This energy-efficient catalytic process utilizes the heat generated by the reaction to self-propagate oligomerization throughout the liquid monomer. FROMO employs a terminal olefin (e.g., styrene) in which a cross-metathesis reaction (i.e., chain transfer) competes with ring-opening metathesis (i.e., propagation). Kendrick mass analysis enables rapid identification and assignment of all the chain-end types present and quantifies the degree of branching resulting from the infrequent cyclopentene ring-opening reaction. This analytical technique also detects oligomer species derived from trace impurities in the monomer or chain-transfer agent that are otherwise difficult to observe with other characterization methods. Here, the obtained oligomers possess well-defined chain-ends and molecular weight distributions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Synthesis and Blending of Two Poly(ethylene- co -vinyl alcohol) Polymers with Mixed 1,2-Diol Stereochemistry

Parallel pathways for the postpolymerization modification of double bonds in a polycyclooctene (PCOE) backbone generate vicinal 1,2-diol-containing polymers with mixed but opposite stereochemistry, depending on the trans:cis ratio of the C═C in PCOE. Beginning from the same batch of PCOE, epoxidation and subsequent ring-opening with sulfuric acid and water produce a polymer with the majority erythro diols, whereas an osmium-catalyzed dihydroxylation results in diols in the majority threo orientations. These postpolymerization modification approaches enable access to previously unexplored polymers with a mixture of erythro and threo diols, offering tunable diol stereochemistry to tailor material properties. The majority erythro diols lead to hexagonal crystallites with higher melting temperatures and overall crystallinity when compared to the majority threo diols that form monoclinic crystallites. When blended, the two diastereomers phase separate as evidenced by distinct melting endotherms and crystal structures corresponding to the two component polymers, suggesting a route to tune the barrier or mechanical properties. Furthermore, this investigation synthesized polymers with mixed stereochemical diols and elucidated the thermal and morphological properties of regioregular linear poly(ethylene-co-vinyl alcohols) and their blends.

1,2-diols↗

DOE OSTI2025

Sustainable upcycling of polyethylene waste to compatibilizers and valuable chemicals

Controllable functionalization of polyethylene (PE) waste could generate new polymeric materials that are generally difficult to manufacture sustainably while also addressing the growing plastics waste problem. However, these modifications remain challenging due to the inherent stability of the PE backbone. Non-thermal atmospheric plasma enables molecular activation under mild conditions while utilizing renewable energy but is primarily employed for surface modification, as plasmas do not penetrate the bulk of materials. Herein, controllable bulk oxidative functionalization of PE wax (PEW) and low-density PE (LDPE) of varying molecular weights was achieved, with up to 6 mol% oxygen incorporation, by manipulating melt viscosity. This functionalization was accomplished either through temperature adjustment or by introducing a melt viscosity modifier, removable via simple extraction methods, to reduce LDPE viscosity, enhance diffusion and chain mobility, and enable bulk oxidation. The oxidized LDPE induces compatibilization in blends of poly(lactic acid) (PLA) and LDPE with improved interfacial adhesion and mechanical properties, such as a 70% increase in elongation-at-break values vs. the control. These findings pave the way for catalyst-free upcycling of direct plastics waste and plastics waste-derived products, enabling the creation of high-value products across various markets.

Plastic upcycling↗

DOE OSTI2022

Outstanding questions on xylan biosynthesis

Xylan is the second most abundant polysaccharide in plant biomass. It is a crucial component of cell wall structure as well as a significant factor contributing to biomass recalcitrance. Xylan consists of a linear chain of β-1,4-linked xylosyl residues that are often substituted with glycosyl side chains, such as glucuronosyl/methylglucuronosyl and arabinofuranosyl residues, and acetylated at O-2 and/or O-3. Xylan from gymnosperms and dicots contains a unique reducing end tetrasaccharide sequence that is not detected in xylan from grasses, bryophytes and seedless vascular plants. Grass xylan is heavily decorated at O-3 with arabinofuranosyl residues that are frequently esterified with hydroxycinnamates. Further, genetic and biochemical studies have uncovered a number of genes involved in xylan backbone elongation and acetylation, xylan glycosyl substitutions and their modifications, and the synthesis of the unique xylan reducing end tetrasaccharide sequence, but some outstanding issues on the biosynthesis of xylan still remain unanswered. Here, we provide a brief overview of xylan structure and focus on discussion of the current understanding and open questions on xylan biosynthesis. Further elucidation of the biochemical mechanisms underlying xylan biosynthesis will not only shed new insights into cell wall biology but also provide molecular tools for genetic modification of biomass composition tailored for diverse end uses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Cytochromes P450 involved in bacterial RiPP biosyntheses

Abstract Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally synthesized proteins and additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 (P450s) are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of P450s distributed across all domains of life. While the number of characterized P450s involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C–C or C–N bond formation. Formation of some RiPPs is catalyzed by more than one P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered. Summary The presence of genes encoding P450s in gene clusters for ribosomally synthesized and post-translationally modified peptides expand structural and functional diversity of these secondary metabolites, and here, we review the current state of this knowledge.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Blocky Selective Postpolymerization C–H Functionalization of Polyolefins

C–H functionalization of commodity polyolefins affords functional materials derived from a high-volume, low-cost resource. However, current postpolymerization modification strategies result in randomly distributed functionalization along the length of the polymer backbone, which has a negative impact on the crystallinity of the resultant polymers, and thus the thermomechanical properties. Here, we demonstrate an amidyl radical mediated C–H functionalization of polyolefins to access blocky microstructures, which exhibit a higher crystalline fraction, larger crystallite size, and improved mechanical properties compared to their randomly functionalized analogues. Taking inspiration from the site-selective C–H functionalization of small molecules, we leverage the steric protection provided by crystallites and target polymer functionalization to amorphous domains in a semicrystalline polyolefin gel. The beneficial outcomes of blocky functionalization are independent of the identity of the pendant functional group that is installed through functionalization. Here, the decoupling of functional group incorporation and crystallinity highlights the promise in accessing nonrandom microstructures through selective functionalization to circumvent traditional tradeoffs in postpolymerization modification, with potential impact in advanced materials and upcycling plastic waste.

Neidhart, Eliza K. [The University of North Caroli↗

DOE OSTI2023

Synthesis and Post-Processing of Chemically Homogeneous Nanothreads from 2,5-Furandicarboxylic Acid

Compared with conventional, solution-phase approaches, solid-state reaction methods can provide unique access to novel synthetic targets. Nanothreads—one-dimensional diamondoid polymers formed through the compression of small molecules—represent a new class of materials produced via solid-state reactions, however, the formation of chemically homogeneous products with targeted functionalization represents a persistent challenge. Through careful consideration of molecular precursor stacking geometry and functionalization, we report here the scalable synthesis of chemically homogeneous, functionalized nanothreads through the solid-state polymerization of 2,5-furandicarboxylic acid. The resulting product possesses high-density, pendant carboxyl functionalization along both sides of the backbone, enabling new opportunities for the post-synthetic processing and chemical modification of nanothread materials applicable to a broad range of potential applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗