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At least 487 records · Page 27

High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes

Photosystem I (PSI) is one of the two main pigment–protein complexes where the primary steps of oxygenic photosynthesis take place. This review describes low-temperature frequency-domain experiments (absorption, emission, circular dichroism, resonant and non-resonant hole-burned spectra) and modeling efforts reported for PSI in recent years. In particular, we focus on the spectral hole-burning studies, which are not as common in photosynthesis research as the time-domain spectroscopies. Experimental and modeling data obtained for trimeric cyanobacterial Photosystem I (PSI 3 ), PSI 3 mutants, and PSI 3 –IsiA 18 supercomplexes are analyzed to provide a more comprehensive understanding of their excitonic structure and excitation energy transfer (EET) processes. Detailed information on the excitonic structure of photosynthetic complexes is essential to determine the structure–function relationship. We will focus on the so-called “red antenna states” of cyanobacterial PSI, as these states play an important role in photochemical processes and EET pathways. The high-resolution data and modeling studies presented here provide additional information on the energetics of the lowest energy states and their chlorophyll (Chl) compositions, as well as the EET pathways and how they are altered by mutations. We present evidence that the low-energy traps observed in PSI are excitonically coupled states with significant charge-transfer (CT) character. The analysis presented for various optical spectra of PSI 3 and PSI 3 -IsiA 18 supercomplexes allowed us to make inferences about EET from the IsiA 18 ring to the PSI 3 core and demonstrate that the number of entry points varies between sample preparations studied by different groups. In our most recent samples, there most likely are three entry points for EET from the IsiA 18 ring per the PSI core monomer, with two of these entry points likely being located next to each other. Therefore, there are nine entry points from the IsiA 18 ring to the PSI 3 trimer. We anticipate that the data discussed below will stimulate further research in this area, providing even more insight into the structure-based models of these important cyanobacterial photosystems.

59 BASIC BIOLOGICAL SCIENCES↗

CYP76BK1 orthologs catalyze furan and lactone ring formation in clerodane diterpenoids across the mint family

The Lamiaceae (mint family) is the largest known source of furanoclerodanes, a subset of clerodane diterpenoids with broad bioactivities including insect antifeedant properties. The Ajugoideae subfamily, in particular, accumulates significant numbers of structurally related furanoclerodanes. The biosynthetic capacity for formation of these diterpenoids is retained across most Lamiaceae subfamilies, including the early-diverging Callicarpoideae which forms a sister clade to the rest of Lamiaceae. VacCYP76BK1, a cytochrome P450 monooxygenase from Vitex agnus-castus, was previously found to catalyze the formation of the proposed precursor to furan and lactone-containing labdane diterpenoids. Through transcriptome-guided pathway exploration, we identified orthologs of VacCYP76BK1 in Ajuga reptans and Callicarpa americana. Functional characterization demonstrated that both could catalyze the oxidative cyclization of clerodane backbones to yield a furan ring. Subsequent investigation revealed a total of 10 CYP76BK1 orthologs across six Lamiaceae subfamilies. Through analysis of available chromosome-scale genomes, we identified four CYP76BK1 members as syntelogs within a conserved syntenic block across divergent subfamilies. This suggests an evolutionary lineage that predates the speciation of the Lamiaceae. Functional characterization of the CYP76BK1 orthologs affirmed conservation of function, as all catalyzed furan ring formation. Additionally, some orthologs yielded two novel lactone ring moieties. The presence of the CYP76BK1 orthologs across Lamiaceae subfamilies closely overlaps with the distribution of reported furanoclerodanes. Together, the activities and distribution of the CYP76BK1 orthologs identified here support their central role in furanoclerodane biosynthesis within the Lamiaceae family. Our findings lay the groundwork for biotechnological applications to harness the economic potential of this promising class of compounds.

59 BASIC BIOLOGICAL SCIENCES↗

Directed Gas-Phase Formation of Azulene (C 10 H 8 ): Unraveling the Bottom-Up Chemistry of Saddle-Shaped Aromatics

The azulene (C 10 H 8 ) molecule, the simplest polycyclic aromatic hydrocarbon (PAH) carrying a fused seven- and five-membered ring, is regarded as a fundamental molecular building block of saddle-shaped carbonaceous nanostructures such as curved nanographenes in the interstellar medium. However, an understanding of the underlying gas-phase formation mechanisms of this nonbenzenoid 10π-Hückel aromatic molecule under low-temperature conditions is in its infancy. Here, by merging crossed molecular beam experiments with electronic structure calculations and molecular dynamics simulations, our investigations unravel an unconventional low-temperature, barrierless route to azulene via the reaction of the simplest organic radical, methylidyne (CH), with indene (C 9 H 8 ) through ring expansion. This reaction might represent the initial step toward to the formation of saddle-shaped PAHs with seven-membered ring moieties in hydrocarbon-rich cold molecular clouds such as the Taurus Molecular Cloud-1 (TMC-1). These findings challenge conventional wisdom that molecular mass growth processes to nonplanar PAHs, especially those containing seven-membered rings, operate only at elevated pressure and high-temperature conditions, thus affording a versatile low-temperature route to contorted aromatics in our galaxy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fatigue performance of the Deeply Embedded Ring Anchor

Existing anchor solutions are limited in their applicability to the floating offshore wind industry, which demands prolonged load endurance in extreme weather conditions and varied seabed soils. This limitation restricts project feasibility and increases costs. In order to address these challenges, the Deeply Embedded Ring Anchor (DERA) is proposed to achieve substantial reductions in anchor costs through efficiency enhancements. Ensuring the long-term safety and reliability of the DERA, especially considering a minimum operational period of 25 years, necessitates a comprehensive understanding of fatigue damage. Induced by repetitive loading below material yield strength, fatigue poses a significant threat to structures exposed to waves and currents. Anchors, vital for station keeping, are susceptible to fatigue damage, particularly in the padeye area. This paper conducts a fatigue analysis, focusing on factors such as the wall thickness of the ring anchor, inner stiffeners, and stiffener thickness, to evaluate the performance of DERA in this context. The results showed that the stiffener significantly affects the elongation of the total life of the anchor. In conclusion, this paper focuses on advancing innovations like DERA, enabling the efficient utilization of offshore wind resources, and addressing safety concerns through meticulous fatigue analysis.

17 WIND ENERGY↗

Structural basis for differential recognition of phosphohistidine-containing peptides by 1-pHis and 3-pHis monoclonal antibodies

In 2015, monoclonal antibodies (mAbs) that selectively recognize the 1-pHis or 3-pHis isoforms of phosphohistidine were developed by immunizing rabbits with degenerate Ala/Gly peptides containing the nonhydrolyzable phosphohistidine (pHis) analog- phosphotriazolylalanine (pTza). Here, we report structures of five rabbit mAbs bound to cognate pTza peptides: SC1-1 and SC50-3 that recognize 1-pHis, and their 3-pHis–specific counterparts, SC39-4, SC44-8, and SC56-2. These cocrystal structures provide insights into the binding modes of the pTza phosphate group that are distinct for the 1- and 3-pHis mAbs with the selectivity arising from specific contacts with the phosphate group and triazolyl ring. The mode of phosphate recognition in the 3-pHis mAbs recapitulates the Walker A motif, as present in kinases. The complementarity-determining regions (CDRs) of four of the Fabs interact with the peptide backbone rather than peptide side chains, thus conferring sequence independence, whereas SC44-8 shows a proclivity for binding a GpHAGA motif mediated by a sterically complementary CDRL3 loop. Specific hydrogen bonding with the triazolyl ring precludes recognition of pTyr and other phosphoamino acids by these mAbs. Kinetic binding experiments reveal that the affinity of pHis mAbs for pHis and pTza peptides is submicromolar. Bound pHis mAbs also shield the pHis peptides from rapid dephosphorylation. The epitope–paratope interactions illustrate how these anti-pHis antibodies are useful for a wide range of research techniques and this structural information can be utilized to improve the specificity and affinity of these antibodies toward a variety of pHis substrates to understand the role of histidine phosphorylation in healthy and diseased states.

59 BASIC BIOLOGICAL SCIENCES↗

Structure and properties of bottlebrush polyelectrolyte complexes

Abstract Structural variation of polyelectrolytes has been shown to play an important role in altering polyelectrolyte complex (PEC) properties in recent years. However, molecular‐level details such as polyelectrolyte architecture remain underdeveloped. Here, we use a combination of ring‐opening metathesis polymerization (ROMP), atom‐transfer radical polymerization (ATRP), and postpolymerization reactions to create densely branched bottlebrushes of poly(dimethylamino ethyl methcacrylate) and poly(tert‐butyl methacrylate) with high molecular weights (MDa), which we then convert into fully charged and densely branched bottlebrushes of poly(trimethylaminoethyl methacrylate) (PTMAEMA) and poly(methacrylic acid) (PAA). We investigate the structure and properties of bottlebrush polyelectrolyte complexes (BPECs) using optical microscopy, rheology, cryogenic transmission electron microscopy (Cryo‐TEM), and small‐angle X‐ray scattering (SAXS). Bottlebrush polyelectrolyte complexes are white solids, which exhibit gel‐like mechanical properties, which we attribute to sidechain interpenetration. Using a combination of Cryo‐TEM and SAXS, we are able to outline the structural development of BPECs, detailing how the network topology, sidechain conformation, and interdigitation spacing changes as a function of salt. Our results provide a foundation for further exploration of branched architectures within polyelectrolyte complexation.

Polymer Science↗

Pentamethylcyclopentadienyl Metalloradical Iron Complexes Containing Redox Noninnocent α-Diimine-Type Ligands: Synthesis, Molecular, and Electronic Structures

The synthesis and characterization of pentamethylcyclopentadienyl iron complexes bearing the redox non-innocent α-diimine (N,N'-dimesitylbutane-2,3-diimine, Mes DI) and α-iminopyridine (N-mesityl(pyridin-2-yl)ethanimine Mes PI) ligands were explored. One-pot reduction and complexation of the cyclopentadienyl ring was accomplished by treatment of (κ 2 -N,N')FeCl 2 (N,N'= Mes DI or Mes PI) pre-cursors with [C 5 Me 5 ]Li. The resulting iron compounds were characterized by paramagnetic 1 H NMR spectroscopy, magnetic susceptibility measurements, zero-field 57 Fe Mössbauer spectroscopy, low-temperature EPR spectroscopy, and cyclic voltammetry. The combined spectroscopic, structural and DFT computational data supported low-spin iron(III) compounds (S Fe = ½) with π-acidic, formally doubly-reduced chelating ligands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization of Two Positional Isomers of the Cs + Gly Complex Using Two-Color, IR–IR Photobleaching of the Cryogenically Cooled Ions

Metal ion binding to amino acid residues is an important interaction motif that controls the tertiary structures of oligopeptides. Analyses of the vibrational band patterns displayed by the amino acid scaffolds are commonly used to characterize the local docking motifs. Here we carry out two-color, IR-IR photobleaching measurements to obtain isomer-selective vibrational spectra of the Cs + Gly ion-molecule complex isolated in a cryogenically cooled, radiofrequency ion trap. The distinct band patterns of two non-interconverting isomers are observed and traced to different bidentate binding motifs between Cs + and the glycine scaffold. In one isomer, the ion attaches to the oxygen atoms of the carboxyl group whereas in the other it docks to the amino nitrogen and the carbonyl oxygen. Attachment to the acid head group yields a very diffuse absorption associated the OH group engaged in a strong intramolecular H-bond that closes a 5 membered ring. Furthermore, the band assignments, rearrangement pathways and electrostatic distortion of the electron density distributions in the glycine scaffold by the proximal ion are explored with electronic structure calculations and anharmonic theory.

Infrared spectroscopy↗

ECAR-8823 Rev 0 Structural Evaluation of the MARVEL Support Frame in Dry Critical Configuration

The purpose of this ECAR is to structurally evaluate the MARVEL reactor support frame during the dry critical (DryCrit) start-up testing. The ECAR includes evaluation of the DryCrit configuration for tip-over of the frame during a seismic event, floor loading of the frame on the MFC-720 (TREAT) operating floor, stress analysis of the adapter ring, and stress analysis of the frame itself for gravity and seismic loads.

21 - SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLAN↗

Gas phase synthesis of the C40 nano bowl C 40 H 10

Nanobowls represent vital molecular building blocks of end-capped nanotubes and fullerenes detected in combustion systems and in deep space such as toward the planetary nebula TC-1, but their fundamental formation mechanisms have remained elusive. By merging molecular beam experiments with electronic structure calculations, we reveal a complex chain of reactions initiated through the gas-phase preparation of benzocorannulene (C 24 H 12 ) via ring annulation of the corannulenyl radical (C 20 H 9 • ) by vinylacetylene (C 4 H 4 ) as identified isomer-selectively in situ via photoionization efficiency curves and photoion mass-selected threshold photoelectron spectra. In silico studies provided compelling evidence that the benzannulation mechanism can be expanded to pentabenzocorannulene (C 40 H 20 ) followed by successive cyclodehydrogenation to the C40 nanobowl (C 40 H 10 ) – a fundamental building block of buckminsterfullerene (C 60 ). This high-temperature pathway opens up isomer-selective routes to nanobowls via resonantly stabilized free-radical intermediates and ring annulation in circumstellar envelopes of carbon stars and planetary nebulae as their descendants eventually altering our insights of the complex chemistry of carbon in our Galaxy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unit-cell-thick zeolitic imidazolate framework films for membrane application

Zeolitic imidazolate frameworks (ZIFs) are a subset of metal–organic frameworks with more than 200 characterized crystalline and amorphous networks made of divalent transition metal centres (for example, Zn 2+ and Co 2+ ) linked by imidazolate linkers. ZIF thin films have been intensively pursued, motivated by the desire to prepare membranes for selective gas and liquid separations. To achieve membranes with high throughput, as in ångström-scale biological channels with nanometre-scale path lengths, ZIF films with the minimum possible thickness—down to just one unit cell—are highly desired. However, the state-of-the-art methods yield membranes where ZIF films have thickness exceeding 50 nm. Here we report a crystallization method from ultradilute precursor mixtures, which exploits registry with the underlying crystalline substrate, yielding (within minutes) crystalline ZIF films with thickness down to that of a single structural building unit (2 nm). The film crystallized on graphene has a rigid aperture made of a six-membered zinc imidazolate coordination ring, enabling high-permselective H 2 separation performance. The method reported here will probably accelerate the development of two-dimensional metal–organic framework films for efficient membrane separation.

36 MATERIALS SCIENCE↗

Comparison of Hafnium Dioxide and Zirconium Dioxide Grown by Plasma-Enhanced Atomic Layer Deposition for the Application of Electronic Materials

We report the growth of nanoscale hafnium dioxide (HfO 2 ) and zirconium dioxide (ZrO 2 ) thin films using remote plasma-enhanced atomic layer deposition (PE-ALD), and the fabrication of complementary metal-oxide semiconductor (CMOS) integrated circuits using the HfO 2 and ZrO 2 thin films as the gate oxide. Tetrakis (dimethylamino) hafnium (Hf[N(CH 3 ) 2 ] 4 ) and tetrakis (dimethylamino) zirconium (IV) (Zr[N(CH 3 ) 2 ] 4 ) were used as the precursors, while O 2 gas was used as the reactive gas. The PE-ALD-grown HfO 2 and ZrO 2 thin films were analyzed using X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), and high-resolution transmission electron microscopy (HRTEM). The XPS measurements show that the ZrO 2 film has the atomic concentrations of 34% Zr, 2% C, and 64% O while the HfO 2 film has the atomic concentrations of 29% Hf, 11% C, and 60% O. The HRTEM and XRD measurements show both HfO 2 and ZrO 2 films have polycrystalline structures. n-channel and p-channel metal-oxide semiconductor field-effect transistors (nFETs and pFETs), CMOS inverters, and CMOS ring oscillators were fabricated to test the quality of the HfO 2 and ZrO 2 thin films as the gate oxide. Current-voltage (IV) curves, transfer characteristics, and oscillation waveforms were measured from the fabricated transistors, inverters, and oscillators, respectively. The experimental results measured from the HfO 2 and ZrO 2 thin films were compared.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

FlbB forms a distinctive ring essential for periplasmic flagellar assembly and motility in Borrelia burgdorferi

Spirochetes are a widespread group of bacteria with a distinct morphology. Some spirochetes are important human pathogens that utilize periplasmic flagella to achieve motility and host infection. The motors that drive the rotation of periplasmic flagella have a unique spirochete-specific feature, termed the collar, crucial for the flat-wave morphology and motility of the Lyme disease spirochete Borrelia burgdorferi. Here, we deploy cryo-electron tomography and subtomogram averaging to determine high-resolution in-situ structures of the B. burgdorferi flagellar motor. Comparative analysis and molecular modeling of in-situ flagellar motor structures from B. burgdorferi mutants lacking each of the known collar proteins (FlcA, FlcB, FlcC, FlbB, and Bb0236/FlcD) uncover a complex protein network at the base of the collar. Importantly, our data suggest that FlbB forms a novel periplasmic ring around the rotor but also acts as a scaffold supporting collar assembly and subsequent recruitment of stator complexes. The complex protein network based on the FlbB ring effectively bridges the rotor and 16 torque-generating stator complexes in each flagellar motor, thus contributing to the specialized motility and lifestyle of spirochetes in complex environments.

59 BASIC BIOLOGICAL SCIENCES↗

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Characterization of SETD3 methyltransferase–mediated protein methionine methylation

Most characterized protein methylation events encompass arginine and lysine N-methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these cases, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain–containing 3 (SETD3) is a protein (i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S-methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr 312 and Trp 273 , as well as the hydrocarbon side chain of Ile 310 . Our results suggest that placing methionine properly in the active site—within close proximity to and in line with the incoming methyl group of SAM—would allow some SET domain proteins to selectively methylate methionine in proteins.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Influence of Ti‐incorporated Zeolite Topology and Pore Condensation on Vapor Phase Propylene Epoxidation Kinetics with Gaseous H 2 O 2

Abstract Vapor‐phase propylene (C 3 H 6 ) epoxidation kinetics with hydrogen peroxide (H 2 O 2 ) strongly reflects the physical properties of Ti‐incorporated zeolite catalysts and the presence of spectating molecules (“solvent”) near active sites even without a bulk liquid phase. Steady‐state turnover rates of C 3 H 6 epoxidation and product selectivities vary by orders of magnitudes, depending on the zeolite silanol ((SiOH) x ) density, pore topology (MFI, *BEA, FAU), and the quantity of condensed acetonitrile (CH 3 CN) molecules nearby active sites, under identical reaction mechanisms sharing activated H 2 O 2 intermediates on Ti surfaces. Individual kinetic analyses for propylene oxide (PO) ring‐opening, homogeneous diol oxidative cleavage, and homogeneous aldehyde oxidation reveal that secondary reaction kinetics following C 3 H 6 epoxidation responds more sensitively to the changes in zeolite physical properties and pore condensation with CH 3 CN. Thus, higher PO selectivities achieved in hydrophilic Ti‐MFI at steady‐state reflect the preferential stabilization of transition states for C 3 H 6 epoxidation (a primary reaction) relative to PO ring‐opening and oxidative cleavage (secondary reactions) that solvation effects that reflect interactions among condensed CH 3 CN within pores and the extended pore structure.

Kwon, Ohsung↗

Quantum Many-Body Theory from a Solution of the N -Representability Problem

Here, in this study, we present a many-body theory based on a solution of the N-representability problem in which the ground-state two-particle reduced density matrix (2-RDM) is determined directly without the many-particle wave function. We derive an equation that re-expresses physical constraints on higher-order RDMs to generate direct constraints on the 2-RDM, which are required for its derivation from an N-particle density matrix, known as N-representability conditions. The approach produces a complete hierarchy of 2-RDM constraints that do not depend explicitly upon the higher RDMs or the wave function. By using the two-particle part of a unitary decomposition of higher order constraint matrices, we can solve the energy minimization by semidefinite programming in a form where the low-rank structure of these matrices can be potentially exploited. We illustrate by computing the ground-state electronic energy and properties of the H 8 ring.

74 ATOMIC AND MOLECULAR PHYSICS↗

Robustness of Optical Response for Self-Assembled Plasmonic Metamaterials with Morphological Disorder and Surface Roughness

Bottom-up fabrication of metallized biotemplated nanostructures to form specific plasmonic nanoresonators holds promise as a means of achieving large-scale optical metamaterials. However, in contrast to top-down methods, the stochastic growth of self-assembled nanoresonators is prone to significant disorder and surface roughness, which naturally raise an important question about the robustness of their resonant properties in terms of structural imperfections. An aggregated-random-sphere model is developed to mimic the nucleated growth of metallized DNA origami assembly, leading to meta-atoms with realistic, experimentally observed morphological disorder and surface roughness. Using the well-known split-ring-resonator (SRR) motif as an example, the resonant properties of meta-atoms under different levels of roughness are investigated and a strong tolerance of optical response against morphological disorder is revealed. It is found that in SRRs, even with dramatic roughness introduced, the expected resonances are still observed, despite broadening line shapes compared to ideal smooth structure. Only for extreme disorder, which causes drastic segmentation of SRRs, does the resonant response disappear. Finally, the demonstrations are very encouraging for the prospects of bottom-up fabrication toward versatile functional metamaterials and metadevices.

36 MATERIALS SCIENCE↗