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At least 55 records · Page 3

Halogenation-Dependent Effects of the Chlorosulfolipids of Ochromonas danica on Lipid Bilayers

The chlorosulfolipids are amphiphilic natural products with stereochemically complex patterns of chlorination and sulfation. Despite their role in toxic shellfish poisoning, potential pharmacological activities, and unknown biological roles, they remain understudied due to the difficulties in purifying them from natural sources. The structure of these molecules, with a charged sulfate group in the middle of the hydrophobic chain, appears incompatible with the conventional lipid bilayer structure. Questions about chlorosulfolipids remain unanswered partly due to the unavailability of structural analogues with which to conduct structure–function studies. Here, we approach this problem by combining enantioselective total synthesis and membrane biophysics. Using a combination of Langmuir pressure–area isotherms of lipid monolayers, fluorescence imaging of vesicles, mass spectrometry imaging, natural product isolation, small-angle X-ray scattering, and cryogenic electron microscopy, we show that danicalipin A (1) likely inserts into lipid bilayers in the headgroup region and alters their structure and phase behavior. Specifically, danicalipin A (1) thins the bilayer and fluidizes it, allowing even saturated lipid to form fluid bilayers. Lipid monolayers show similar fluidizing upon insertion of danicalipin A (1). Furthermore, we show that the halogenation of the molecule is critical for its membrane activity, likely due to sterically controlled conformational changes. Synthetic unchlorinated and monochlorinated analogues do not thin and fluidize lipid bilayers to the same extent as the natural product. Overall, this study sheds light on how amphiphilic small molecules interact with lipid bilayers and the importance of stereochemistry and halogenation for this interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Copper-Binding Peptide with Therapeutic Potential against Alzheimer′s Disease: From the Blood–Brain Barrier to Metal Competition

Alzheimer’s disease (AD) is the most common form of dementia worldwide. AD brains are characterized by the accumulation of amyloid-β peptides (Aβ) that bind Cu 2+ and have been associated with several neurotoxic mechanisms. Although the use of copper chelators to prevent the formation of Cu 2+ -Aβ complexes has been proposed as a therapeutic strategy, recent studies show that copper is an important neuromodulator that is essential for a neuroprotective mechanism mediated by Cu 2+ binding to the cellular prion protein (PrPC). Therefore, in addition to metal selectivity and blood–brain barrier (BBB) permeability, an emerging challenge for copper chelators is to prevent the formation of neurotoxic Cu 2+ -Aβ species without perturbing the neuroprotective Cu 2+ -PrPC interaction. Previously, we reported the design of a tetrapeptide (TP) that withdraws Cu 2+ from Aβ(1–16) and impacts the Cu 2+ -induced aggregation of Aβ(1–40). In this study, we improved the drug-like properties of TP in a BBB model, evaluated the metal selectivity of the optimized peptide (TP*), and tested its effect on Cu 2+ coordination to PrPC and proteins involved in copper trafficking, such as copper transporter 1 and albumin. Our results show that changing the stereochemistry of the first residue prevents TP degradation in the BBB model and coadministration of TP with a peptide that increases BBB permeability allows its passage through the BBB model. TP* is highly selective toward Cu 2+ in the presence of Zn 2+ ions, transfers Cu 2+ to copper-trafficking proteins, and forms a ternary TP*-Cu 2+ -PrP species that does not perturb the physiological conformation of PrP and displays only a minor impact in the neuroprotective Cu 2+ -dependent interaction of PrPC with the N-methyl-d-aspartate receptor. Overall, these results show that TP* displays desirable features for a copper chelator with therapeutic potential against AD. Moreover, this is the first study that explores the effect of a Cu 2+ chelator with therapeutic potential for AD on Cu 2+ coordination to PrPC (an emerging key player in AD pathology), integrating recent knowledge about metalloproteins involved in AD with the design of copper chelators against AD.

60 APPLIED LIFE SCIENCES↗

Coupling of Flavonoid Initiation Sites with Monolignols Studied by Density Functional Theory

Lignin recalcitrance presents a challenge for the development of a bioeconomy that employs lignocellulosic feedstocks. The efficiency of lignin deconstruction is improved by a reduction of molecular weight, and given the discovery that flavones serve as initiation sites in lignin biosynthesis, these molecular weight reductions could potentially be achieved with plant metabolic engineering to over-express flavonoids. Upon increasing the flavonoid content in lignin, the bond strengths and properties of flavonoid-monolignol linkages become increasingly important. To that end, the current work applies density functional theory calculations to elucidate the bond dissociation enthalpies (BDEs) of flavonoid-monolignol linkages, including dimers with oxidized monolignols. Specifically, the dimer bond strengths and monomer hydrogen abstraction energies for the flavonoids tricin, chrysoeriol, luteolin, apigenin, catechin, epicatechin, epigallocatechin, and epigallocatechin gallate are calculated, when coupled to seven natural and engineered monolignols. Results indicate that 4'-O-ß linkage strengths between flavonoids and monolignols are of comparable strength to inter-monolignol ß-O-4 linkages, with average flavonoid-monolignol BDEs of 70.7 kcal/mol relative to ~69.3 kcal/mol in analogous canonical monolignols. Epigallocatechin yielded the lowest 4'-O-ß bond strength of 52.3 kcal/mol when coupled to an oxidized monolignol, while the flavones overall produced lower average BDEs, relative to the flavanols. Substituents at the 3'-C and 5'-C positions on flavonoids affected the dimer linkage strengths to a greater extent than glycosylation or substituents further from the linkage. Erythro and threo stereochemistry across the flavonoid-monolignol linkage library exhibited only small energetic differences and no pronounced correlations. Taken together, the predictions from this work support the concept that higher concentrations of flavonoid initiation sites in lignin may afford linkage properties conducive to more facile lignin depolymerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Insights into the Conversion of Biorenewable Levoglucosanol to Dideoxysugars

Here, a molecular understanding of the conversion of biorenewable threo- and erythro-levoglucosanol (LGOL) to 3,4-dideoxysugars in aqueous medium is provided based on first-principles simulations. The synthetic importance of this transformation is that these intermediates can be quantitatively hydrogenated to (S,S)/(S,R) hexane-1,2,5,6-tetrol (tetrol), whose stereochemistry depends on which dideoxy sugar intermediates are formed during LGOL conversion. The thermodynamic and kinetic feasibility of the acetal (R 2 C(OR) 2 ) hydrolysis in LGOL is investigated via computing the free energy profile. In aqueous medium, the rate-determining step of LGOL hydrolysis is the protonation of the anhydro-bridge oxygen atom of LGOL concurrent with ring opening, yielding the cyclic forms of 3,4-dideoxymannose (DDM) and 3,4-dideoxyglucose (DDG) from threo- and erythro-LGOL, respectively. The measured activation energies of LGOL hydrolysis are 20.5 and 23.6 kcal/mol for DDM and DDG formation, respectively. These values are in agreement with the computed protonation free energies of 17.1 and 18.2 kcal/mol, respectively. Based on the simulations, a Bronsted base-catalyzed isomerization from DDG or DDM to 3,4-dideoxy fructose (DDF) is preferred with lower apparent activation free energy barriers compared to the acid-catalyzed isomerization. In summary, this study provides mechanistic information about the conversion of the biomass-derived anhydro-sugar LGOL to 3,4-dideoxy sugars, which are precursors to renewable high-value chemicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Butene-Rich Alkene Formation from 2,3-Butanediol through Dioxolane Intermediates

The cost-effective production of sustainable aviation fuels (SAF) remains a major challenge within the energy sector. One approach to address this is the fermentation of biomass feedstocks into oxygenates followed by catalytic conversion to alkenes or other oligomerization precursors. 2,3-Butanediol (BDO) is a promising fermentation product due to its four-carbon nature, its decreased microorganism toxicity and associated higher maximum fermentation titers relative to other alcohols and oxygenates, and its capacity to be readily converted into butene isomers and longer chain alkenes. BDO conversion is currently constrained by separation challenges for BDO isolation due to its high boiling point and hydrophilicity. Here, this work expands upon previous BDO reactive separation via dioxolane formation over a solid acid catalyst by investigating the conversion of dioxolanes into alkene mixtures. Dioxolanes were formed from a range of aldehydes and subsequently converted over a Cu/ZSM-5 catalyst (448–523 K) via an ether cleavage, hydrogenation, and dehydration reaction network to form alkene-rich product mixtures (96% C 3+ alkene yield, 523 K). This selectivity is greater than that of direct BDO conversion to alkenes over an identical catalyst (89%, 523 K). C 3+ alkene selectivity is maximized between 498 and 523 K at complete dioxolane conversion without significant alkene hydrogenation to alkanes. The alkene product distributions can be tailored via both aldehyde selection during dioxolane formation and the dioxolane conversion reaction temperature. Alkene mixtures from dioxolane conversion predominantly reflect the carbon chain length and stereochemistry of BDO and the initial aldehyde at or below 498 K, yet higher reaction temperatures yield alkene mixtures of similar carbon chain distributions, regardless of initial aldehyde selection. Deactivation of the Cu/ZSM-5 catalyst is observed for multiple steps of the overall reaction network but can be minimized by facilitating the complete dioxolane-to-alkene reaction network at temperatures of at least 498 K.

2,3-butanediol↗

Catalytic Dynamic Kinetic Resolutions in Tandem to Construct Two-Axis Terphenyl Atropisomers

The defined structure of molecules bearing multiple stereogenic axes is of increasing relevance to materials science, pharmaceuticals, and catalysis. However, catalytic enantioselective approaches to control multiple stereogenic axes remain synthetically challenging. Here, we report the catalytic synthesis of two-axis terphenyl atropisomers, with complementary strategies to both chlorinated and brominated variants, formed with high diastereo- and enantioselectivity. The chemistry proceeds through a sequence of two distinct dynamic kinetic resolutions: first, an atroposelective ring opening of Bringmann-type lactones produces a product with one established axis of chirality, and second, a stereoselective arene halogenation delivers the product with the second axis of chirality established. In order to achieve these results, a class of Brønsted basic guanidinylated peptides, which catalyze an efficient atroposelective chlorination, is reported for the first time. In addition, a complementary bromination is reported, which also establishes the second stereogenic axis. These bromo-terphenyls are accessible following the discovery that chiral anion phase transfer catalysis by C 2 -symmetric phosphoric acids allows catalyst control in the second stereochemistry-determining event. Accordingly, we established the fully catalyst-controlled stereodivergent synthesis of all possible chlorinated stereoisomers while also demonstrating diastereodivergence in the brominated variants, with significant levels of enantioselectivity in all cases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Precise Synthesis of Complex Si–Si Molecular Frameworks

In this Perspective, we highlight the emergence of target-oriented syntheses of complex molecules composed of Si–Si (oligosilanes) rather than C–C bonds. Saturated oligosilanes structurally resemble alkanes with respect to a tetrahedral geometry, a preference for a staggered conformation in linear chains, the ability to form stable small rings, and tetrahedral stereochemistry at asymmetrically functionalized Si centers. There are also critical differences, for example, differences in multiple bonding and the ability to form penta- and hexacoordinated structures, that mean that chemical reactivity and, in particular, rules for stereoselective synthesis do not cleanly translate from carbon to silicon. This Perspective will discuss recent achievements in the precise, controlled synthesis of complex molecules comprised mainly of Si–Si bonds and highlight the mechanistic insights enabling increased molecular complexity. New tools, such as electrochemical and catalytic reactions, will be discussed as well as the problem of controlling relative configuration in molecules containing multiple stereogenic-at-silicon centers. Furthermore, these synthetic achievements facilitate the discovery of new properties, including insight into light absorption, conformation, and mechanical properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Insight into Fluorocarbon Adsorption in Pore Expanded Metal–Organic Framework Analogs

The rapid growth in the global energy demand for space cooling requires the development of more efficient environmental chillers for which adsorption-based cooling systems can be utilized. Here, in this contribution, we explore sorbents for chiller use via a pore-engineering concept to construct analogs of the 1-dimensional pore metal–organic framework MOF-74 by using elongated organic linkers and stereochemistry control. The prepared pore-engineered MOFs show remarkable equilibrium adsorption of the selected fluorocarbon refrigerant that is translated to a modeled adsorption-based refrigeration cycle. To probe molecular level interactions at the origin of these unique adsorption properties for this series of Ni-MOFs, we combined in situ synchrotron X-ray powder diffraction, neutron powder diffraction, X-ray absorption spectroscopy, calorimetry, Fourier transform infrared techniques, and molecular simulations. Our results reveal the coordination of fluorine (of CH2F in R134a) to the nickel(II) open metal centers at low pressures for each Ni-MOF analog and provide insight into the pore filling mechanism for the full range of the adsorption isotherms. The newly designed Ni-TPM demonstrates exceptional R134a adsorption uptake compared to its parent microporous Ni-MOF-74 due to larger engineered pore size/volume. The application of this adsorption performance toward established chiller conditions yields a working capacity increase for Ni-TPM of about 400% from that of Ni-MOF-74, which combined with kinetics directly correlates to both a higher coefficient of performance and a higher average cooling capacity generated in a modeled chiller.

Zheng, Jian↗

Stereodivergent photobiocatalytic radical cyclization through the repurposing and directed evolution of fatty acid photodecarboxylases

Despite their intriguing photophysical and photochemical activities, naturally occurring photoenzymes have not yet been repurposed for new-to-nature activities. Here we engineered fatty acid photodecarboxylases (FAPs) to catalyse unnatural photoredox radical C–C bond formation by leveraging strongly oxidizing excited-state flavoquinone cofactor. Through genome mining, rational engineering and directed evolution, we developed a panel of radical photocyclases (RAPs) to facilitate decarboxylative radical cyclisation with excellent chemo-, enantio-, and diastereoselectivities. Our high-throughput experimental workflow allowed for the directed evolution of FAPs. An orthogonal set of RAPs was engineered to access all four possible stereoisomers of stereochemical dyad, affording fully diastereo- and enantiodivergent biotransformations in asymmetric radical biocatalysis. Molecular dynamics simulations show that our evolved RAPs allow near-attack conformations to be easily accessed, enabling chemoselective radical cyclisation. The development of stereoselective RAPs provides unnatural C–C bond forming activities in natural photoenzyme families, which can be used to tame the stereochemistry of free radical-mediated reactions.

Ju, Shuyun (ORCID:000000020322104X)↗

Structural and compositional complexities of hierarchical self-assembly: A hypergraph approach

Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. In this work, we introduce a hypergraph-based formalism, Blocks & Bonds (B&B), which generalizes classical chemical graph theory by incorporating directed and multicolored interactions, internal symmetries, and hierarchical organization. Within this framework, we develop the Structure Code (SC), a compact and versatile language for describing self-assembled architectures. We define a Kolmogorov-style structural complexity as the total information content of SC, obtained through its tokenization and Shannon information assignment. Complementing this encoding-based measure, we introduce a much simpler quantity, the compositional complexity, which depends only on the number and cumulative usage of block and bond types in the construction set. A central result of this work is a strong empirical correlation between the token-based structural complexity and the compositional complexity across all examined systems. Owing to this agreement, the compositional complexity emerges as the most practical and broadly applicable measure: it is easy to compute, requires no explicit encoding, and yet closely tracks the actual information content of structurally diverse architectures. Applications to molecular systems (ethylene glycol and glucose), DNA-origami lattices, and crystalline assemblies show that B&B hypergraphs provide a unified, scalable, and information-efficient representation of structural organization, naturally capturing symmetry, modularity, and stereochemistry. This framework establishes a quantitative foundation for complexity-aware classification and inverse design of programmable matter.

36 MATERIALS SCIENCE↗

Genomics of sorghum local adaptation to a parasitic plant

Host–parasite coevolution can maintain high levels of genetic diversity in traits involved in species interactions. In many systems, host traits exploited by parasites are constrained by use in other functions, leading to complex selective pressures across space and time. Here, we study genome-wide variation in the staple crop Sorghum bicolor (L.) Moench and its association with the parasitic weed Striga hermonthica (Delile) Benth., a major constraint to food security in Africa. We hypothesize that geographic selection mosaics across gradients of parasite occurrence maintain genetic diversity in sorghum landrace resistance. Suggesting a role in local adaptation to parasite pressure, multiple independent loss-of-function alleles at sorghum LOW GERMINATION STIMULANT 1 (LGS1) are broadly distributed among African landraces and geographically associated with S. hermonthica occurrence. However, low frequency of these alleles within S. hermonthica-prone regions and their absence elsewhere implicate potential trade-offs restricting their fixation. LGS1 is thought to cause resistance by changing stereochemistry of strigolactones, hormones that control plant architecture and below-ground signaling to mycorrhizae and are required to stimulate parasite germination. Consistent with trade-offs, we find signatures of balancing selection surrounding LGS1 and other candidates from analysis of genome-wide associations with parasite distribution. Experiments with CRISPR–Cas9-edited sorghum further indicate that the benefit of LGS1-mediated resistance strongly depends on parasite genotype and abiotic environment and comes at the cost of reduced photosystem gene expression. Our study demonstrates long-term maintenance of diversity in host resistance genes across smallholder agroecosystems, providing a valuable comparison to both industrial farming systems and natural communities.

59 BASIC BIOLOGICAL SCIENCES↗

In situ ligand restraints from quantum-mechanical methods

In macromolecular crystallographic structure refinement, ligands present challenges for the generation of geometric restraints due to their large chemical variability, their possible novel nature and their specific interaction with the binding pocket of the protein. Quantum-mechanical approaches are useful for providing accurate ligand geometries, but can be plagued by the number of minima in flexible molecules. In an effort to avoid these issues, the Quantum Mechanical Restraints (QMR) procedure optimizes the ligand geometry in situ , thus accounting for the influence of the macromolecule on the local energy minima of the ligand. The optimized ligand geometry is used to generate target values for geometric restraints during the crystallographic refinement. As demonstrated using a sample of >2330 ligand instances in >1700 protein–ligand models, QMR restraints generally result in lower deviations from the target stereochemistry compared with conventionally generated restraints. In particular, the QMR approach provides accurate torsion restraints for ligands and other entities.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of switchgrass ( Panicum virgatum L.) PvKSL1 as a levopimaradiene/abietadiene‐type diterpene synthase

Abstract The diverse class of plant diterpenoid metabolites serves important functions in mediating growth, chemical defence, and ecological adaptation. In major monocot crops, such as maize (Zea mays), rice (Oryza sativa), and barley (Hordeum vulgare), diterpenoids function as core components of biotic and abiotic stress resilience. Switchgrass (Panicum virgatum) is a perennial grass valued as a stress‐resilient biofuel model crop. Previously we identified an unusually large diterpene synthase family that produces both common and species‐specific diterpenoids, several of which accumulate in response to abiotic stress. Here, we report discovery and functional characterization of a previously unrecognized monofunctional class I diterpene synthase (PvKSL1) viain vivoco‐expression assays with different copalyl pyrophosphate (CPP) isomers, structural and mutagenesis studies, as well as genomic and transcriptomic analyses. In particular, PvKSL1 convertsent‐CPP intoent‐abietadiene,ent‐palustradiene,ent‐levopimaradiene, andent‐neoabietadiene via a 13‐hydroxy‐8(14)‐ent‐abietene intermediate. Notably, although featuring a distinctent‐stereochemistry, this product profile is near‐identical to bifunctional (+)‐levopimaradiene/abietadiene synthases occurring in conifer trees. PvKSL1 has three of four active site residues previously shown to control (+)‐levopimaradiene/abietadiene synthase catalytic specificity. However, mutagenesis studies suggest a distinct catalytic mechanism in PvKSL1. Genome localization ofPvKSL1distant from other diterpene synthases, and its phylogenetic distinctiveness from known abietane‐forming diterpene synthases, support an independent evolution of PvKSL1 activity. Albeit at low levels,PvKSL1gene expression predominantly in roots suggests a role of diterpenoid formation in belowground tissue. Together, these findings expand the known chemical and functional space of diterpenoid metabolism in monocot crops.

Plant Sciences↗

Dual activity of anthocyanidin reductase supports the dominant plant proanthocyanidin extension unit pathway

Proanthocyanidins (PAs) are plant natural products important for agriculture and human health. They are polymers of flavan-3-ol subunits, commonly (-)-epicatechin and/or (+)-catechin, but the source of the in planta extension unit that comprises the bulk of the polymer remains unclear, as does how PA composition is determined in different plant species. Anthocyanidin reductase (ANR) can generate 2,3-cis-epicatechin as a PA starter unit from cyanidin, which itself arises from 2,3-trans-leucocyanidin, but ANR proteins from different species produce mixtures of flavan-3-ols with different stereochemistries in vitro. Genetic and biochemical analyses here show that ANR has dual activity and is involved not only in the production of (-)-epicatechin starter units but also in the formation of 2,3-cis-leucocyanidin to serve as (-)-epicatechin extension units. Differences in the product specificities of ANRs account for the presence/absence of PA polymerization and the compositions of PAs across plant species.

59 BASIC BIOLOGICAL SCIENCES↗

Flyby reaction trajectories: Chemical dynamics under extrinsic force

Dynamic effects are an important determinant of chemical reactivity and selectivity, but the deliberate manipulation of atomic motions during a chemical transformation is not straightforward. In this work, we demonstrate that extrinsic force exerted upon cyclobutanes by stretching pendant polymer chains influences product selectivity through force-imparted nonstatistical dynamic effects on the stepwise ring-opening reaction. The high product stereoselectivity is quantified by carbon-13 labeling and shown to depend on external force, reactant stereochemistry, and intermediate stability. Computational modeling and simulations show that, besides altering energy barriers, the mechanical force activates reactive intramolecular motions nonstatistically, setting up “flyby trajectories” that advance directly to product without isomerization excursions. A mechanistic model incorporating nonstatistical dynamic effects accounts for isomer-dependent mechanochemical stereoselectivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Vernier template synthesis of molecular knots

Molecular knots are often prepared using metal helicates to cross the strands. Here we found that coordinatively mismatching oligodentate ligands and metal ions provides a more effective way to synthesize larger knots using Vernier templating. Strands composed of different numbers of tridentate 2,6-pyridinedicarboxamide groups fold around nine-coordinate lanthanide (III) ions to generate strand-entangled complexes with the lowest common multiple of coordination sites for the ligand strands and metal ions. Ring-closing olefin metathesis then completes the knots. A 3:2 (ditopic strand:metal) Vernier assembly produces +3 1 #+3 1 and –3 1 #–3 1 granny knots. Vernier complexes of 3:4 (tetratopic strand:metal) stoichiometry selectively form a 378-atom-long trefoil-of-trefoils triskelion knot with 12 alternating strand crossings or, by using opposing stereochemistry at the terminus of the strand, an inverted-core triskelion knot with six alternating and six nonalternating strand crossings.

74 ATOMIC AND MOLECULAR PHYSICS↗

Lithographic crystallinity regulation in additive fabrication of thermoplastics (CRAFT)

For semicrystalline polyolefin thermoplastics, the balance between interconnected ordered crystalline and disordered amorphous regions is paramount to their performance and processability. However, contemporary manufacturing strategies, from injection molding to three-dimensional (3D) printing, result in monolithic objects, unable to spatially encode crystallinity. We develop a light-based approach for fabricating mechanically robust polyolefin thermoplastics with microscopic control over crystallinity in 3D space. Light dosage governs polymer stereochemistry giving access to a continuum of materials, from strong rigid plastics, such as high-density polyethylene, to more extensible materials akin to low-density polyethylene, all at the flick of a switch. Leveraging this finding in lithographic grayscale 3D printing enables rapid multimaterial fabrication with voxel-level control over optical and mechanical properties, opening avenues in information storage, soft robotics, and energy damping.

36 MATERIALS SCIENCE↗

Architector

Architector is a 3D chemical structure generation software package designed to take minimal 2D information about ligands and metal centers and generates chemically sensible 3D conformers and stereochemistry of the organometallic compounds. Architector is capable of high-throughput in-silico construction of s-, p-, d-, and f-block organometallic complexes. Architector represents a transformative step towards cross-periodic table computational design of metal complex chemistry.

Yang, Ping↗