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At least 1,261 records · Page 70

Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX

The G-quadruplex (GQ) is a well-studied non-canonical DNA structure formed by G-rich sequences found at telomeres and gene promoters. Biological studies suggest that GQs may play roles in regulating gene expression, DNA replication, and DNA repair. Small molecule ligands were shown to alter GQ structure and stability and thereby serve as novel therapies, particularly against cancer. In this work, we investigate the interaction of a G-rich sequence, 5’-GGGTTGGGTTGGGTTGGG-3’ (T1), with a water-soluble porphyrin, N- methyl mesoporphyrin IX (NMM) via biophysical and X-ray crystallographic studies. UV-vis and fluorescence titrations, as well as a Job plot, revealed a 1:1 binding stoichiometry with an impressively tight binding constant of 30–50 μM -1 and ΔG 298 of -10.3 kcal/mol. Eight extended variants of T1 (named T2 –T9) were fully characterized and T7 was identified as a suitable candidate for crystallographic studies. We solved the crystal structures of the T1- and T7-NMM complexes at 2.39 and 2.34 Å resolution, respectively. Both complexes form a 5’-5’ dimer of parallel GQs capped by NMM at the 3’ G-quartet, supporting the 1:1 binding stoichiometry. Our work provides invaluable details about GQ-ligand binding interactions and informs the design of novel anticancer drugs that selectively recognize specific GQs and modulate their stability for therapeutic purposes.

59 BASIC BIOLOGICAL SCIENCES↗

Metadynamics simulations reveal mechanisms of Na + and Ca 2+ transport in two open states of the channelrhodopsin chimera, C1C2

Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca 2+ permeability vs. Na + by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na + and Ca 2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca 2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biophysical and biochemical evidence for the role of acetate kinases (AckAs) in an acetogenic pathway in pathogenic spirochetes

Unraveling the metabolism of Treponema pallidum is a key component to understanding the pathogenesis of the human disease that it causes, syphilis. For decades, it was assumed that glucose was the sole carbon/energy source for this parasitic spirochete. But the lack of citric-acid-cycle enzymes suggested that alternative sources could be utilized, especially in microaerophilic host environments where glycolysis should not be robust. Recent bioinformatic, biophysical, and biochemical evidence supports the existence of an acetogenic energy-conservation pathway in T . pallidum and related treponemal species. In this hypothetical pathway, exogenous D-lactate can be utilized by the bacterium as an alternative energy source. Herein, we examined the final enzyme in this pathway, acetate kinase (named TP0476), which ostensibly catalyzes the generation of ATP from ADP and acetyl-phosphate. We found that TP0476 was able to carry out this reaction, but the protein was not suitable for biophysical and structural characterization. We thus performed additional studies on the homologous enzyme (75% amino-acid sequence identity) from the oral pathogen Treponema vincentii , TV0924. This protein also exhibited acetate kinase activity, and it was amenable to structural and biophysical studies. We established that the enzyme exists as a dimer in solution, and then determined its crystal structure at a resolution of 1.36 Å, showing that the protein has a similar fold to other known acetate kinases. Mutation of residues in the putative active site drastically altered its enzymatic activity. A second crystal structure of TV0924 in the presence of AMP (at 1.3 Å resolution) provided insight into the binding of one of the enzyme’s substrates. On balance, this evidence strongly supported the roles of TP0476 and TV0924 as acetate kinases, reinforcing the hypothesis of an acetogenic pathway in pathogenic treponemes.

Deka, Ranjit K.↗

Cbp1, a fungal virulence factor under positive selection, forms an effector complex that drives macrophage lysis

Intracellular pathogens secrete effectors to manipulate their host cells. Histoplasma capsulatum (Hc) is a fungal intracellular pathogen of humans that grows in a yeast form in the host. Hc yeasts are phagocytosed by macrophages, where fungal intracellular replication precedes macrophage lysis. The most abundant virulence factor secreted by Hc yeast cells is Calcium Binding Protein 1 (Cbp1), which is absolutely required for macrophage lysis. Here we take an evolutionary, structural, and cell biological approach to understand Cbp1 function. We find that Cbp1 is present only in the genomes of closely related dimorphic fungal species of the Ajellomycetaceae family that lead primarily intracellular lifestyles in their mammalian hosts (Histoplasma, Paracoccidioides, and Emergomyces), but not conserved in the extracellular fungal pathogen Blastomyces dermatitidis. We observe a high rate of fixation of non-synonymous substitutions in the Cbp1 coding sequences, indicating that Cbp1 is under positive selection. We determine the de novo structures of Hc H88 Cbp1 and the Paracoccidioides americana (Pb03) Cbp1, revealing a novel “binocular” fold consisting of a helical dimer arrangement wherein two helices from each monomer contribute to a four-helix bundle. In contrast to Pb03 Cbp1, we show that Emergomyces Cbp1 orthologs are unable to stimulate macrophage lysis when expressed in the Hc cbp1 mutant. Consistent with this result, we find that wild-type Emergomyces africanus yeast are able to grow within primary macrophages but are incapable of lysing them. Finally, we use subcellular fractionation of infected macrophages and indirect immunofluorescence to show that Cbp1 localizes to the macrophage cytosol during Hc infection, making this the first instance of a phagosomal human fungal pathogen directing an effector into the cytosol of the host cell. We additionally show that Cbp1 forms a complex with Yps-3, another known Hc virulence factor that accesses the cytosol. Taken together, these data imply that Cbp1 is a fungal virulence factor under positive selection that localizes to the cytosol to trigger host cell lysis.

59 BASIC BIOLOGICAL SCIENCES↗

Structure and antigenicity of the divergent human astrovirus VA1 capsid spike

Human astrovirus (HAstV) is a known cause of viral gastroenteritis in children worldwide, but HAstV can cause also severe and systemic infections in immunocompromised patients. There are three clades of HAstV: classical, MLB, and VA/HMO. While all three clades are found in gastrointestinal samples, HAstV-VA/HMO is the main clade associated with meningitis and encephalitis in immunocompromised patients. To understand how the HAstV-VA/HMO can infect the central nervous system, we investigated its sequence-divergent capsid spike, which functions in cell attachment and may influence viral tropism. Here we report the high-resolution crystal structures of the HAstV-VA1 capsid spike from strains isolated from patients with gastrointestinal and neuronal disease. The HAstV-VA1 spike forms a dimer and shares a core beta-barrel structure with other astrovirus capsid spikes but is otherwise strikingly different, suggesting that HAstV-VA1 may utilize a different cell receptor, and an infection competition assay supports this hypothesis. Furthermore, by mapping the capsid protease cleavage site onto the structure, the maturation and assembly of the HAstV-VA1 capsid is revealed. Finally, comparison of gastrointestinal and neuronal HAstV-VA1 sequences, structures, and antigenicity suggests that neuronal HAstV-VA1 strains may have acquired immune escape mutations. Overall, our studies on the HAstV-VA1 capsid spike lay a foundation to further investigate the biology of HAstV-VA/HMO and to develop vaccines and therapeutics targeting it.

60 APPLIED LIFE SCIENCES↗

Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition

Copy-out/paste-in transposition is a major bacterial DNA mobility pathway. It contributes significantly to the emergence of antibiotic resistance, often by upregulating expression of downstream genes upon integration. Unlike other transposition pathways, it requires both asymmetric and symmetric strand transfer steps. Here, we report the first structural study of a copy-out/paste-in transposase and demonstrate its ability to catalyze all pathway steps in vitro. X-ray structures of ISCth4 transposase, a member of the IS256 family of insertion sequences, bound to DNA substrates corresponding to three sequential steps in the reaction reveal an unusual asymmetric dimeric transpososome. During transposition, an array of N-terminal domains binds a single transposon end while the catalytic domain moves to accommodate the varying substrates. These conformational changes control the path of DNA flanking the transposon end and the generation of DNA-binding sites. Our results explain the asymmetric outcome of the initial strand transfer and show how DNA binding is modulated by the asymmetric transposase to allow the capture of a second transposon end and to integrate a circular intermediate.

59 BASIC BIOLOGICAL SCIENCES↗

Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome

Cristae are high–curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae–shaping proteins have been defined, analogous lipid–based mechanisms have yet to be elucidated. Here, we combine experimental lipidome dissection with multi–scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the inner mitochondrial membrane against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein–mediated curvatures. This model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that cardiolipin is essential in low–oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of cardiolipin is dependent on the surrounding lipid and protein components of the IMM.

59 BASIC BIOLOGICAL SCIENCES↗

Development of Chromium and Sulfur Getter for Solid Oxide Fuel Cell (SOFC) System

Under the “real world” SOFC operating conditions, gaseous Cr and S species coexist in air stream. The combined Cr and S effect on the electrochemical poisoning of candidate LSM and LSCF electrodes has been investigated. Electrochemical and structural analysis revealed that the combined Cr and S interactions with the LSCF electrode remains significantly different from those of the individual Cr and S interactions. S reacts with the surface SrO accompanied by morphological changes whereas the hexavalent gaseous Cr species mainly deposit at the LSCF/GDC interface as is the case with Cr-only poisoning. For LSM electrode, the combined interactions of Cr and S remains similar to the sum of individual Cr and S effects as SO 2 reacts with Sr-rich regions of the bulk LSM, while Cr deposits at the electrochemically active sites. The use of getter, consisting of alkaline earth and transition metal oxides, has been proposed as a cost-effective approach to mitigate electrode poisoning. SrMnO 3 (SMO) is suggested as a robust getter material for the co-capture of airborne gaseous S and Cr species entering high-temperature electrochemical systems. The honeycomb getter forms, covered with SMO nanoparticles, were fabricated using dip coating. The SMO getter successfully maintained the electrochemical activity of LSM under the presence of gaseous Cr and S species, validating the efficacy of the getter. Post-test characterization revealed that the absorption of S and Cr contaminants led to the elongation of granular SMO particles, forming SrO nanorods and SrCrO 4 whiskers leaving Mn oxides underneath where inward-migrating Cr reside, indicating the high mutual affinity of Sr and Mn. The growth of reaction products during the long term exposure favors continued absorption of incoming S and Cr contaminants. The Mn 2 O 9 dimers, existing on the surface, are considered to help absorb S and Cr impurities, along with the Sr-terminated surface. The SMO getter also displays robust stability in humid environments at high temperatures without phase transformation or hydrolysis, fulfilling the requirement for operation in high-temperature electrochemical systems.

30 DIRECT ENERGY CONVERSION↗

Chemical Thermodynamic Modeling of Molten Salts to Support Off-Gas Abatement Systems

The reprocessing of used nuclear fuel by any means will liberate gaseous fission products, such as hydrogen ( 3 H), carbon ( 14 C), noble gases ( 85 Kr), and halogens ( 129 I), from the irradiated fuel. These elements will distribute through chemical processing operations and partition into process off-gas streams, and the specific volatile release fractions will be dictated by the chemical and physical properties of the system. A recent assessment found that there were significant knowledge gaps regarding the release quantities of volatile radionuclides from individual unit operations. These knowledge gaps limited the ability to determine what dedicated off-gas treatment technologies could be required for electrochemical-based reprocessing facilities. Unfortunately, experimental efforts to quantify release fractions are limited by the challenges associated with performing experiments using irradiated fuel. This report documents preliminary thermodynamic predictions of iodine and tritium release from chloride-based molten salts as part of an effort to better direct resources toward those experiments (both simulant and irradiated) that will be of the greatest impact. It was predicted that less than 0.5% of tritium was expected to be released and that nearly all of that amount would be released as H 2 . Thermochemical data for hydrogen (H 2 ) are of high fidelity, and no additional validation is recommended. Less than 0.05% of iodine was predicted to be released, with the primary volatile species being Cs 2 I 2 . Unlike the tritium predictions, the data underpinning the iodine release predictions are of low quality. It is recommended that a limited experimental program be dedicated to expanding the current physical property and thermodynamic property data for iodine in electrochemical processing and molten salt conditions, including vapor pressure measurements for the dimerized species predicted to comprise the majority of iodine release. Validating and improving the thermodynamic properties used in predictive modeling can reduce the need for expensive testing with irradiated fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

System Integration of Rationally Designed Dilute Alloy Catalysts for Energy-Efficient Electrochemical CO 2 -To-Fuel Conversion

Energy effiecient electrochemical conversion of CO 2 to high-demand chemicals and transportation fuels using renewable solar and wind energy is a key technology needed for a high-productivity, low-carbon future. However, the development of scalable, low-cost, active, selective, and stable electrocatalysts remains a key challenge that needs to be overcome to enable high-volume conversion of CO 2 to feedstock chemicals for the chemical industry. In previous work, Lawrence Livermore National Laboratory (LLNL) has developed a rational design platform for dilute alloy transition metal electrocatalysts that promise to make electrochemical CO 2 conversion more energy efficient and selective. In this project, we worked with our industrial partners, Twelve and TotalEnergies, to improve scale up, integration, and stability of LLNL’s dilute alloy catalyst technology into an industry-relevant zero gap electrolyzer platform. Through virtual experiments and data analysis, we designed efficient and cost-effective copper-based catalysts. The catalyst was specifically designed to streamline the slowest and most energy-intensive step of the electrochemical chemical transformation of CO 2 to multi-carbon products – that is making the carbon-carbon bond by dimerization of the reaction intermediate carbon monoxide - resulting in up to 10% improvement in energy efficiency for C 2 products while simultaneously increasing the selectivity towards C 2 products. We tested two different scalable catalyst coating technologies and down-selected magnetron sputtering as the technique that provided the best control over catalyst loading, composition, and morphology. Using this technology, we successfully demonstrated integration of our dilute alloy catalysts into a 100 cm 2 electrolyzer platform with Faradaic efficiencies for ethylene production reaching 40% at a current density of 200 mA/cm 2 . We also developed the technology to integrate a well-defined nanoscale porosity by depositing alloy compositions that were compatible with dealloying, that is, selective leaching of an alloy component to generate nanoscale porosity. We observed that integration of the dealloying-derived nanoporosity improved catalyst performance and stability by leading to a more hydrophobic catalyst/anion exchange membrane interface. Unsolved problems that still need to be addressed are corrosion of the Cu catalyst -specifically if the used catalyst is exposed to air - as well as long term stability do to salt formation/deposition and flooding of the catalyst/electrolyzer flow channels, especially at higher current densities. As we only worked on optimization of catalyst composition, coating thickness, and morphology, further performance optimization will require a system level approach that includes optimization of electrolyzer design and membrane technology.

36 MATERIALS SCIENCE↗

Fabricating Single Crystal Quantum Dot Solids

The central goal of this research program was to establish fundamental synthesis and processing principles to enable the fabrication of single crystal quantum dot solids (QDS) with programmable structure (i.e., hexagonal and square) and composition. Our approach towards that goal leveraged access to and experience with unique in-situ, multi-probe characterization techniques to understand and ultimately control the fundamental relationship between processing conditions and nucleation and growth of QDS. The program integrated synthesis and fabrication (Hanrath) with in-situ TEM analysis (Kourkoutis) and computational modeling (Clancy) to gain atomic-level insights into the underlying physical phenomena governing assembly and attachment and to guide the development of optimized processing methods. We have established a foundational understanding of physicochemical interactions of self-assembly at a fluid interface, superlattice structure transformation pathways, the critical role of disorder during the initial dimerization of colloidal quantum dot monomers, and the residual strain distribution within the inter-dot epitaxial bridge which hampers the formation of novel electronics states of the quantum dot solids. Collectively, these insights have contributed towards advancing the mechanistic understanding of the complex choreography of assembly and attachment as well as understanding what currently limits further advances in high-fidelity quantum dot solids and tiles.

36 MATERIALS SCIENCE↗

Theoretical studies of chemical reactions related to the formation and growth of polycyclic aromatic hydrocarbons (PAH) and molecular properties of their key intermediates (Final Progress Report)

The formation mechanisms of polycyclic aromatic hydrocarbons, (PAHs) – organic molecules carrying fused benzene rings – are of great interest to scientists and engineers due to their importance in combustion chemistry and astrochemistry. On Earth, PAHs are largely produced in incomplete combustion of fossil fuel and are considered as critical precursors to unwanted soot particles leading to combustion inefficiency and causing air pollution along with detrimental health effects. Simple PAH molecules initially formed in the gas phase, are further involved in a build-up process in combustion flames leading to larger PAH, bowl-shaped nanostructures, fullerenes, and solid-phase species including carbonaceous dust, graphene particles, and soot. In deep space, PAH and their derivatives are potential key intermediates and nucleation sites leading eventually to carbonaceous nanoparticles (“interstellar grains”). Therefore, the understanding of the key processes in the synthesis of PAHs along with their precursors and their degradation mechanisms in combustion systems and in interstellar, circumstellar, and planetary atmospheric environments will provide critical insights into how complex aromatic structures, carbonaceous nanoparticles, and fullerenes are formed and destroyed. Achieving this understanding is an important step in the development of the efficient combustion processes and of the ecofriendly devices with reduced environmental pollution as well as technological strategies for the production of hydrogen and solid carbon through thermal or plasma-assisted pyrolysis of natural gas and biomass. Also, the understanding of the key processes of PAH and soot growth will help in our comprehension of chemical evolution in the universe. Detailed information on the mechanisms and reliable rate constants of the key elementary chemical reactions involved in PAH formation and destruction processes and in inception of soot particles is often missing, with the main deficiencies being the absence of temperature- and pressure-dependent rate constants for the broad range of conditions occurring in various terrestrial and interstellar processes and the lack of data on the reaction products and their branching ratios. Complementary to experimental studies, these gaps in knowledge can be filled by using quantum chemical calculations of reaction potential energy surfaces providing us with accurate energies of reaction products, intermediates, and transition states, revealing the reaction mechanism, and giving the molecular properties required to compute rate constants for relevant reaction steps and product branching ratios using the RRKM-Master Equation (ME) method. Molecular dynamics (MD) simulations can be used in cases when a reaction rate cannot be properly described by statistical theories. During the terminal renewal project period we employed these ab initio/RRKM-ME and MD approaches to complete our studies on several key reactions relevant to the formation/growth of PAH and inception of soot particles including (1) the reaction mechanism and kinetics of the resonance stabilized fulvenallenyl radical with propargyl and C 3 H 4 isomers; (2) the reaction mechanism and kinetics for the C + indene and C 2 + styrene reactions producing naphthyl or azulenyl radicals in low-temperature environments; (3) the MD study of non-equilibrium dimerization of acepyrene and coronene and its radical. The information derived from our theoretical calculations contributed to a better fundamental understanding of the reaction mechanisms and provide missing critical kinetic data to improve combustion models of hydrocarbon fuels and astrochemical models of the growth of carbonaceous molecules and particles in cold molecular clouds, circumstellar envelopes, and planetary atmospheres.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Studying Open Quantum Systems Relevant to Chemistry on a Trapped-Ion Quantum Simulator (Final Technical Report)

This project advances the trapped-ion quantum simulator as a versatile platform for studying open quantum system phenomena. We aim to contribute to the emerging quantum simulation toolkits and enable simulation of nanoscale energy processes. Trapped-ion platforms offer unique capabilities: their vibrational motion can be precisely manipulated, measured, and coherently coupled to auxiliary qubits. The vibrational mode can function both as a highly sensitive quantum sensor and a programmable environment bath. Using this platform, we achieved three major outcomes. First, we demonstrated using the vibrational mode as an ultrasensitive probe for testing fundamental physics, including possible nonlinear quantum mechanics effects. Second, we established that these modes can act as controllable baths in which tunable noise and loss can enhance or modify energy-transfer dynamics, providing the experimental preparation toward studying mechanisms relevant to chemical reactions and light-harvesting systems. Third, by introducing controllable nonlinear gain and loss, we showed theoretically how simulations using trapped ions can model vibrationally-assisted energy transport in a non‐Hermitian quantum system comprising a chromophore dimer weakly coupled to a vibrational mode. Exploring the non‐Hermitian dynamics of the whole system including vibrations, we found that energy transfer accompanied by absorption of phonons from a vibrational mode can be significantly enhanced near an exceptional point. This theoretical work on simulation of energy transfer processes in driven non‐Hermitian quantum systems revealed an interesting novel path to study open quantum systems dynamics under conditions of gain and loss. We then further explored the benefits of controllable gain and loss with an experimental realization of quantum analogs of nonlinear oscillators, namely, the van der Pol oscillator. Here we observed mutual synchronization mediated by collective dissipation between two oscillators. In parallel, we explored related quantum networking protocols using the same trapped-ion platform, developing fast, high-fidelity schemes for distributing entanglement. Together, these achievements show that trapped-ion vibrational modes provide a highly programmable and high-fidelity platform for investigating complex dissipative quantum behavior, while enabling new approaches to remote quantum sensing, energy science, and nonlinear quantum dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

"Lignin First" Catalytic Biomass Fractionation: Cooperative Research and Development (Final Report)

In this work, a continuous zwitterionic chromatography using simulated moving beds will be conducted to separate Li and Mg from brines. The existing program that ExxonMobil is carrying out with Clariant and Genomatica is consistent with all pioneer cellulosic fuels plants inasmuch as biomass enters the facility and is processed, in its entirety, through at least the hydrolysis step of biochemical conversion. This approach creates significant operating challenges as biomass can vary widely in composition and mechanical properties across and within a given biomass type. The proposed program involves a first step fractionation using solvolysis and reductive catalysis to generate a lignin oil containing well-defined monomers, dimers, and oligomers and a delignified cellulose/ hemicellulose pulp. The amount of lignin oil vs pulp and the type of monomers produced are expected to vary with biomass type due to differences in lignin composition and chemistry.

09 BIOMASS FUELS↗

Singlet Fission

This report summarizes key findings from DOE Award DE‑SC0007004 – Singlet Fission, documenting more than a decade of research led by Professor Josef Michl. The project advanced foundational understanding of singlet fission (SF) through integrated synthetic, spectroscopic, crystallographic, and computational studies. Across a diverse set of chromophores—including tetracenes, cibalackrot derivatives, BODIPY dimers, TDPPs, and fluorinated isobenzofurans—the team identified structural and packing features that enable or inhibit SF, clarified the roles of charge‑transfer intermediates and excimer formation, and developed simplified theoretical models and computational screening tools for predicting optimal geometries and excited‑state-energetics. The work significantly broadened design principles for SF‑active materials and provided insights relevant to next‑generation solar energy conversion and molecular photophysics.

14 SOLAR ENERGY↗

Nickel Binding to the c-Src SH3 Domain Facilitates Crystallization

Introduction: Numerous X-ray crystal structures of the c-Src SH3 domain have provideda large sampling of atomic-level information for this important signaling domain. Multiple crystalforms have been reported, with variable crystal lattice contacts and chemical crystallizationconditions. Materials and Methods: We crystallized the c-Src SH3 domain in a crystallization buffercontaining NiCl2. Results: A unique crystal structure of the Src SH3 domain in the trigonal space group H32 isdetermined to 1.45 Å resolution. Crystal packing and anomalous scattering reveal that this crystalform is mediated by two ordered nickel ions provided by the crystallization buffer. Nickelcoordination occurs in a 2:2 stoichiometry, which dimerizes two SH3 domain monomers across apseudo-twofold rotation axis and involves the native N-terminal c-Src SH3 amino acid sequence, asurface-exposed histidine residue, and ordered water molecules. Discussion: This study provides an example of metal-mediated crystallization and metal binding byN-terminal protein residues, contrasting with the Amino-Terminal Copper and Nickel Binding(ATCUN) motif. Conclusion: Alternative avenues help widen the potential for future crystallography-based studiesof the c-Src SH3 domain.

Biochemistry & Molecular Biology↗

Qubit Regularization of Quantum Field Theories

To study quantum field theories on a quantum computer, we must begin with Hamiltonians defined on a finite-dimensional Hilbert space and then take appropriate limits. This approach can be seen as a new type of regularization for quantum field theories, which we refer to as qubit regularization. A related finite-dimensional regularization, known as the D-theory approach, was proposed long ago as a general framework for all quantum field theories. In this framework, the dimensionality of the local Hilbert space at each spatial point can increase as needed through an additional flavor index. To reproduce asymptotically free QFTs, most studies assume that qubit-regularized theories require extending the local Hilbert space to infinity. However, contrary to this common belief, recent discoveries in (1+1) dimensions have revealed two examples where asymptotic freedom appears to emerge within a strictly finite-dimensional local Hilbert space through a novel renormalization group (RG) flow. These findings motivate further investigation into whether asymptotically free gauge theories could also emerge within a strictly finite-dimensional local Hilbert space. To support these explorations, we propose an orthonormal basis called the monomer-dimer-tensor-network (MDTN) basis and use it to construct new types of qubit-regularized lattice gauge theories.

Chandrasekharan, Shailesh [Duke Univ., Durham, NC ↗

Alkali Metal Cation Effects for Rapid C–H Activation by Iron(0) Complexes

C–H oxidative addition is a key reaction in organometallic catalysis, motivating efforts to accelerate it. Here, we examine an anionic beta-diketiminate-supported iron(0) species that was previously observed to activate C-H bonds with Na(15-crown-5), but not with K(18-crown-6) or Rb(18-crown-6). Though crown ethers are usually seen as beneficial due to their ability to solubilize alkali metal cations, we observe that removing the crown ether leads to rapid and complete oxidative addition of the C-H bond even by K, Rb, and Cs. The products are iron(II) phenyl hydride complexes that exist as dimers bridged by the alkali metals. Neutron crystallography of the cesium complex verifies the presence and location of the bridging hydrides. It is likely that the crown-free alkali metal cations have greater Lewis acidity that enables them to facilitate oxidative addition of the C-H bond. This system gives insight on how to control the rate and favorability of C-H activation through manipulation of the countercation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗