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At least 379 records · Page 21

A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins

Abstract Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of 3d/4p Mixing on 1s2p Resonant Inelastic X-ray Scattering: Electronic Structure of Oxo-Bridged Iron Dimers

1s2p resonant inelastic X-ray scattering (1s2p RIXS) has proven successful in the determination of the differential orbital covalency (DOC, the amount of metal vs ligand character in each d molecular orbital) of highly covalent centrosymmetric iron environments including heme models and enzymes. However, many reactive intermediates have noncentrosymmetric environments, e.g., the presence of strong metal-oxo bonds, which results in the mixing of metal 4p character into the 3d orbitals. This leads to significant intensity enhancement in the metal K-pre-edge and as shown here, the associated 1s2p RIXS features, which impact their insight into electronic structure. Binuclear oxo bridged high spin Fe(III) complexes are used to determine the effects of 4p mixing on 1s2p RIXS spectra. In addition to developing the analysis of 4p mixing on K-edge XAS and 1s2p RIXS data, this study explains the selective nature of the 4p mixing that also enhances the analysis of L-edge XAS intensity in terms of DOC. These 1s2p RIXS biferric model studies enable new structural insight from related data on peroxo bridged biferric enzyme intermediates. The dimeric nature of the oxo bridged Fe(III) complexes further results in ligand-to-ligand interactions between the Fe(III) sites and angle dependent features just above the pre-edge that reflect the superexchange pathway of the oxo bridge. Lastly, we present a methodology that enables DOC to be obtained when L-edge XAS is inaccessible and only 1s2p RIXS experiments can be performed as in many metalloenzyme intermediates in solution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Selective Detection of Intermediate-Amplitude Motion by Solid-State NMR

The coexistence of rigid and mobile molecules or molecular segments abounds in biomolecular assemblies. Examples include the carbohydrate-rich cell walls of plants and intrinsically disordered proteins that contain rigid β-sheet cores. In solid-state nuclear magnetic resonance (NMR) spectroscopy, dipolar polarization transfer experiments are well suited for detecting rigid components, whereas scalar-coupling experiments are well suited for detecting highly mobile components. However, few NMR methods are available to detect the segments that undergo intermediate-amplitude fast motion. Here, we introduce two NMR experiments, a two-dimensional T 2H -filtered CP-hCH correlation and a three-dimensional J-INADEQUATE CCH correlation, to observe this intermediate-amplitude motion. Both experiments involve 1 H detection under fast magic-angle spinning (MAS). By combining 1 H transverse relaxation (T 2H ) filters with dipolar polarization transfer, we suppress the signals of both highly rigid and highly mobile species, thus revealing the signals of intermediate mobile species. 1 H detection under fast MAS is crucial for distinguishing the different motional amplitudes. Here, we demonstrate these techniques on several plant cell wall samples and show that they allow the selective detection and resolution of certain hemicellulose and pectin signals, which are usually masked by the signals of the rigid cellulose and the highly dynamic pectins in purely dipolar and scalar NMR spectra.

59 BASIC BIOLOGICAL SCIENCES↗

Two-bond 13 C– 13 C spin-coupling constants in saccharides: dependencies on exocyclic hydroxyl group conformation

Seven doubly 13 C-labeled isotopomers of methyl β-D-glucopyranoside, methyl β-D-xylopyranoside, methyl β-D-galactopyranoside, methyl β-D-galactopyranosyl-(1→4)-β-D-glucopyranoside and methyl β-D-galactopyranosyl-(1→4)-β-D-xylopyranoside were prepared, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13 C NMR spectroscopy to determine experimentally the dependence of 2 J C1,C3 values in aldopyranosyl rings on the C1–C2–O2–H torsion angle, θ 2 , involving the C2 carbon of the C1–C2–C3 coupling pathway. Using X-ray crystal structures to determine θ 2 in crystalline samples and by selecting compounds that exhibit a relatively wide range of θ 2 values in the crystalline state, 2 J C1,C3 values measured in crystalline samples were plotted against θ 2 and the resulting plot compared to that obtained from density functional theory (DFT) calculations. For θ 2 values ranging from ~90° to ~240°, very good agreement was observed between the experimental and theoretical plots, providing strong validation of DFT-calculated spin-coupling dependencies on exocyclic C–O bond conformation involving the central carbon of geminal C–C–C coupling pathways. we report that these findings provide new experimental evidence supporting the use of 2 J CCC values as non-conventional spin-coupling constraints in MA'AT conformational modeling of saccharides in solution, and the use of NMR spin-couplings not involving coupled hydroxyl hydrogens as indirect probes of C–O bond conformation. Solvomorphism was observed in crystalline βGal-(1→4)-βGlcOCH 3 wherein the previously-reported methanol solvate form was found to spontaneously convert to a monohydrate upon air-drying, leading to small but discernible conformational changes in, and a new crystalline form of, this disaccharide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

General tensor structure for electron scattering in terms of invariant responses

The general structure of semi-inclusive polarized electron scattering from polarized spin-1/2 targets is developed for use at all energy scales, from modest-energy nuclear physics applications to use in very high energy particle physics. The leptonic and hadronic tensors that enter in the formalism are constructed in a general covariant way in terms of kinematic factors that are frame dependent but model independent and invariant response functions which contain all of the model-dependent dynamics. In the process of developing the general problem the relationships to the conventional responses expressed in terms of the helicity components of the exchanged virtual photon are presented. For semi-inclusive electron scattering with polarized electrons and polarized spin-1/2 targets one finds that 18 invariant response functions are required, each depending on four Lorentz scalar invariants. Additionally it is shown how the semi-inclusive cross sections are related via integrations over the momentum of the selected coincidence particle and sums over open channels.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Parametrizations of the spin density matrix

Highlights: • Proposed two methods for parametrizing the SDM of spinning, unstable particles. • All non-negativity conditions fulfilled; adaptability to various constraints. • First method: based on a theorem; applicable in a simple and flexible way. • Second method: particularly suitable for especial conditions. • Applications: two of them interesting in the search for new physics. We propose for the spin density matrix two parametrizations which automatically fulfill the non-negativity conditions, without setting any bound on the parameters. The first one relies on a theorem, that we prove, and it is rather simple and easily adaptable to some specific reactions, where, for example, parity is conserved or angular momentum conservation entails selection rules. Moreover, in the case when the rank is less than the order of the density matrix, we show how to improve the fits to the data, either by implementing previous suggestions, or by elaborating an alternative method, for which we prove a second theorem. Our second parametrization is a variant of previous treatments, it appears suitable for some particular processes. Moreover, we discuss about the possibility of inferring the elements of the density matrix from the differential decay width. Last, we illustrate various examples of current interest, both in strong and weak decays; some of them may be helpful in the investigation of physics beyond the standard model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Alternant Hydrocarbon Diradicals as Optically Addressable Molecular Qubits

High-spin molecules allow for bottom-up qubit design and are promising platforms for magnetic sensing and quantum information science. Optical addressability of molecular electron spins has also been proposed in first-row transition-metal complexes via optically detected magnetic resonance (ODMR) mechanisms analogous to the diamond-nitrogen-vacancy color center. However, significantly less progress has been made on the front of metal-free molecules, which can deliver lower costs and milder environmental impacts. At present, most luminescent open-shell organic molecules are π-diradicals, but such systems often suffer from poor ground-state open-shell characters necessary to realize a stable ground-state molecular qubit. In this work, we use alternancy symmetry to selectively minimize radical–radical interactions in the ground state, generating π-systems with high diradical characters. We call them m-dimers, referencing the need to covalently link two benzylic radicals at their meta carbon atoms for the desired symmetry. Through a detailed electronic structure analysis, we find that the excited states of alternant hydrocarbon m-diradicals contain important symmetries that can be used to construct ODMR mechanisms leading to ground-state spin polarization. Furthermore, the molecular parameters are set in the context of a tris(2,4,6-trichlorophenyl)methyl (TTM) radical dimer covalently tethered at the meta position, demonstrating the feasibility of alternant m-diradicals as molecular color centers.

Chemistry↗

Quantum Sensing of Electric Fields Using Spin-Correlated Radical Ion Pairs

Quantum sensing affords the possibility of using quantum entanglement to probe electromagnetic fields with exquisite sensitivity. In this work, we show that a photogenerated spin-correlated radical ion pair (SCRP) can be used to sense an electric field change created at one radical ion of the pair using molecular recognition. The SCRP is generated within a covalent donor–chromophore–acceptor system PXX–PMI–NDI, 1, where PXX = peri-xanthenoxanthene, PMI = 1,6-bis(p-t-butylphenoxy)perylene-3,4-dicarboximide, and NDI = naphthalene-1,8:4,5-bis(dicarboximide). The electron-rich PXX donor in 1 acts as a guest molecule that can be encapsulated selectively by a tetracationic cyclophane ExBox4+ host to give a supramolecular complex 1 ⊂ ExBox 4+ . Selective photoexcitation of the PMI chromophore results in ultrafast generation of the PXX •+ –PMI–NDI •– SCRP. When PXX is encapsulated by ExBox 4+ , the cyclophane generates an electric field that repels the positive charge on PXX •+ within PXX •+ –PMI–NDI •– , reducing the SCRP distance, i.e., the distance between the centers-of-charge on the donor and acceptor. Pulse-EPR measurements are used to measure the coherent oscillations created primarily by the electron–electron dipolar coupling in the SCRP, which yields the distance between the two charges (spins) of PXX •+ –PMI–NDI •– . Here, the experimental results show that the distance between PXX •+ and NDI •– decreases when ExBox 4+ encapsulates PXX •+ , which demonstrates that the SCRP can function as a quantum sensor to detect electric field changes in the vicinity of the radical ions.

Anions↗

Block copolymer self-assembly to pattern gold nanodots for site-specific placement of DNA origami and attachment of nanomaterials

Directed placement of DNA origami could play a key role in future integrated nanoelectronic devices. Here we demonstrated the site-selective attachment of DNA origami on gold dots formed using a pattern transfer method through block copolymer self-assembly. First, a random copolymer brush layer is grafted on the Si surface and then poly (styrene-b-methylmethacrylate) block copolymer is spin-coated to give a hexagonal nanoarray after annealing. UV irradiation followed by acetic acid etching is used to remove the PMMA, creating cylindrical holes and then oxygen plasma etching removes the random copolymer layer inside those holes. Next, metal evaporation, followed by lift-off creates a gold dot array. We evaluated different ligand functionalization of Au dots, as well as DNA hybridization to attach DNA origami to the nanodots. DNA-coated Au nanorods are assembled on the DNA origami as a step towards creating nanowires and to facilitate electron microscopy characterization of the attachment of DNA origami on these Au nanodots. The DNA hybridization approach showed better DNA attachment to Au nanodots than localization by electrostatic interaction. Here, this work contributes to the understanding of DNA-templated assembly, nanomaterials, and block copolymer nanolithography. Furthermore, the work shows potential for creating DNA-templated nanodevices and their placement in ordered arrays in future nanoelectronics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Efficiency of charge transfer in changing the dissociation dynamics of OD + transients formed after the photo-fragmentation of D 2 O

Here, we present an investigation of the relaxation dynamics of deuterated water molecules after direct photo-double ionization at 61 eV. We focus on the very rare D + + O + + D reaction channel in which the sequential fragmentation mechanisms were found to dominate the dynamics. Aided by theory, the state-selective formation and breakup of the transient OD + (a 1 Δ, b 1 Σ + ) is traced, and the most likely dissociation path—OD + : a 1 Δ or b 1 Σ + → A 3 Π → X 3 Σ – → B 3 Σ – —involving a combination of spin–orbit and non-adiabatic charge transfer transitions is determined. The multi-step transition probability of this complex transition sequence in the intermediate fragment ion is directly evaluated as a function of the energy of the transient OD + above its lowest dissociation limit from the measured ratio of the D + + O + + D and competing D + + D + + O sequential fragmentation channels, which are measured simultaneously. Our coupled-channel time-dependent dynamics calculations reproduce the general trends of these multi-state relative transition rates toward the three-body fragmentation channels.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multigas Adsorption with Single-Site Cooperativity in a Metal-Organic Framework

Cooperative gas adsorption in metal-organic frameworks (MOFs) is a rare phenomenon that generally involves long-range communication between multiple binding sites. We demonstrate a MOF containing cobalt(II)-methyl sites that selectively and reversibly capture two carbon monoxide (CO) molecules per site, leading to record-high adsorption capacities at ambient temperatures and pressures. Gas adsorption and structural, spectroscopic, and computational analyses support a mechanism in which binding of one CO molecule triggers a spin transition, followed by binding of a second CO molecule and migratory insertion of the first CO molecule into the cobalt-methyl bond to form an acetyl. The greater binding affinity associated with the second CO results in sigmoidal adsorption isotherms, a hallmark of cooperativity and phase-change materials, despite the absence of long-range interactions within the framework.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interfacial stabilization for epitaxial CuCrO 2 delafossites

AB O 2 delafossites are fascinating materials that exhibit a wide range of physical properties, including giant Rashba spin splitting and anomalous Hall effects, because of their characteristic layered structures composed of noble metal A and strongly correlated B O 2 sublayers. However, thin film synthesis is known to be extremely challenging owing to their low symmetry rhombohedral structures, which limit the selection of substrates for thin film epitaxy. Hexagonal lattices, such as those provided by Al 2 O 3 (0001) and (111) oriented cubic perovskites, are promising candidates for epitaxy of delafossites. However, the formation of twin domains and impurity phases is hard to suppress, and the nucleation and growth mechanisms thereon have not been studied for the growth of epitaxial delafossites. In this study, we report the epitaxial stabilization of a new interfacial phase formed during pulsed-laser epitaxy of (0001)-oriented CuCrO 2 epitaxial thin films on Al 2 O 3 substrates. Through a combined study using scanning transmission electron microscopy/electron-energy loss spectroscopy and density functional theory calculations, we report that the nucleation of a thermodynamically stable, atomically thick CuCr 1-x Al x O 2 interfacial layer is the critical element for the epitaxy of CuCrO 2 delafossites on Al 2 O 3 substrates. This finding provides key insights into the thermodynamic mechanism for the nucleation of intermixing-induced buffer layers that can be used for the growth of other noble-metal-based delafossites, which are known to be challenging due to the difficulty in initial nucleation.

36 MATERIALS SCIENCE↗

Star-forming S0 galaxies in the SDSS-IV MaNGA survey

ABSTRACT To investigate star-forming activities in early-type galaxies, we select a sample of 52 star-forming S0 galaxies (SFS0s) from the SDSS-IV MaNGA survey. We find that SFS0s have smaller stellar masses compared to normal S0s in MaNGA. After matching the stellar mass to select the control sample, we find that the mean Sérsic index of SFS0 bulges (1.76 ± 0.21) is significantly smaller than that of the control sample (2.57 ± 0.20), suggesting the existence of pseudo-bulges in SFS0s. After introducing the environmental information, SFS0s show smaller spin parameters in the field than in groups, while the control sample has no obvious difference in different environments, which may suggest different dynamical processes in SFS0s. Furthermore, with derived N/O and O/H abundance ratios, SFS0s in the field show nitrogen enrichment, providing evidence for the accretion of metal-poor gas in the field environment. To study the star-formation relation, we show that the slope of the spatially resolved star-formation main sequence is nearly 1.0 with MaNGA integral field unit data, confirming the self-regulation of star-formation activity on kpc scales.

79 ASTRONOMY AND ASTROPHYSICS↗

Emulator-Based Bayesian Calibration of the CISNET Colorectal Cancer Models

Purpose To calibrate Cancer Intervention and Surveillance Modeling Network (CISNET)'s SimCRC, MISCAN-Colon, and CRC-SPIN simulation models of the natural history colorectal cancer (CRC) with an emulator-based Bayesian algorithm and internally validate the model-predicted outcomes to calibration targets.Methods We used Latin hypercube sampling to sample up to 50,000 parameter sets for each CISNET-CRC model and generated the corresponding outputs. We trained multilayer perceptron artificial neural networks (ANNs) as emulators using the input and output samples for each CISNET-CRC model. We selected ANN structures with corresponding hyperparameters (i.e., number of hidden layers, nodes, activation functions, epochs, and optimizer) that minimize the predicted mean square error on the validation sample. We implemented the ANN emulators in a probabilistic programming language and calibrated the input parameters with Hamiltonian Monte Carlo-based algorithms to obtain the joint posterior distributions of the CISNET-CRC models' parameters. We internally validated each calibrated emulator by comparing the model-predicted posterior outputs against the calibration targets.Results The optimal ANN for SimCRC had 4 hidden layers and 360 hidden nodes, MISCAN-Colon had 4 hidden layers and 114 hidden nodes, and CRC-SPIN had 1 hidden layer and 140 hidden nodes. The total time for training and calibrating the emulators was 7.3, 4.0, and 0.66 h for SimCRC, MISCAN-Colon, and CRC-SPIN, respectively. The mean of the model-predicted outputs fell within the 95% confidence intervals of the calibration targets in 98 of 110 for SimCRC, 65 of 93 for MISCAN, and 31 of 41 targets for CRC-SPIN.Conclusions Using ANN emulators is a practical solution to reduce the computational burden and complexity for Bayesian calibration of individual-level simulation models used for policy analysis, such as the CISNET CRC models. In this work, we present a step-by-step guide to constructing emulators for calibrating 3 realistic CRC individual-level models using a Bayesian approach.

artificial neural networks↗

Glauber-Theory Calculations of High-Energy Nuclear Scattering Observables Using Variational Monte Carlo Wave Functions

Experiments using intermediate- to high-energy radioactive nuclear beams present numerous findings. Extracting important properties of physical observables relies on a firm theoretical analysis. Though Glauber theory is believed to work well, no convincing calculation has so far been done. Here, we perform ab initio Glauber theory calculations of both elastic differential cross sections and total reaction cross sections for p+ 12 C, 12 C+ 12 C, and 6 He+ 12 C systems. The wave functions of both 6 He and 12 C are generated by variational Monte Carlo calculations with spatial and spin-isospin correlations induced by realistic two- and three-nucleon potentials. Glauber’s phase-shift function is computed by Monte Carlo integration up to all orders of nucleon-nucleon multiple scatterings. We show an excellent performance of the Glauber description to the selected data on the above systems. We also find that the cumulant expansion of the phase-shift function converges rapidly up to the second order for the above systems. This finding will open up interesting applications for the analysis of high-energy nuclear experiments.

Horiuchi, W. [Osaka Metropolitan University (Japan↗

Topological Spin Textures in an Insulating van der Waals Ferromagnet

Generation and control of topological spin textures constitutes one of the most exciting challenges of modern spintronics given their potential applications in information storage technologies. Of particular interest are magnetic insulators, which due to low damping, absence of Joule heating and reduced dissipation can provide energy-efficient spin-textures platform. Here, it is demonstrated that the interplay between sample thickness, external magnetic fields, and optical excitations can generate a prolific paramount of spin textures, and their coexistence in insulating CrBr 3 van der Waals (vdW) ferromagnets. Using high-resolution magnetic force microscopy and large-scale micromagnetic simulation methods, the existence of a large region in T-B phase diagram is demonstrated where different stripe domains, skyrmion crystals, and magnetic domains exist and can be intrinsically selected or transformed to each-other via a phase-switch mechanism. Lorentz transmission electron microscopy unveils the mixed chirality of the magnetic textures that are of Bloch-type at given conditions but can be further manipulated into Néel-type or hybrid-type via thickness-engineering. The topological phase transformation between the different magnetic objects can be further inspected by standard photoluminescence optical probes resolved by circular polarization indicative of an existence of exciton-skyrmion coupling mechanism. The findings identify vdW magnetic insulators as a promising framework of materials for the manipulation and generation of highly ordered skyrmion lattices relevant for device integration at the atomic level.

36 MATERIALS SCIENCE↗

Nature Versus Nurture: A Bayesian Framework for Assessing Apparent Correlations between Planetary Orbital Properties and Stellar Ages

Many exoplanets have orbital characteristics quite different from those seen in our own solar system, including planets locked in orbital resonances and planets on orbits that are elliptical or highly inclined from their host star’s spin axis. It is debated whether the wide variety in system architecture is primarily due to differences in formation conditions (nature) or due to evolution over time (nurture). Identifying trends between planetary and stellar properties, including stellar age, can help distinguish between these competing theories and offer insights as to how planets form and evolve. However, it can be challenging to determine whether observed trends between planetary properties and stellar age are driven by the age of the system—pointing to evolution over time being an important factor—or other parameters to which the age may be related, such as stellar mass or stellar temperature. The situation is complicated further by the possibilities of selection biases, small number statistics, uncertainties in stellar age, and orbital evolution timescales that are typically much shorter than the range of observed ages. Here, we develop a Bayesian statistical framework to assess the robustness of such observed correlations and to determine whether they are indeed due to evolutionary processes, are more likely to reflect different formation scenarios, or are merely coincidental. We apply this framework to reported trends between stellar age and 2:1 orbital resonances, spin–orbit misalignments, and hot Jupiters’ orbital eccentricities. We find strong support for the nurture hypothesis only in the final case.

79 ASTRONOMY AND ASTROPHYSICS↗

Mechanisms of Complete Dissociation of CO 2 on Iron Clusters

Dissociation of CO 2 on iron clusters was studied by using semilocal density functional theory and basis sets of triple-zeta quality. Fe 2 , Fe 4 , and Fe 16 clusters were selected as the representative host clusters. When searching for isomers of Fe n CO 2 , n=2, 4 and 16 corresponding to carbon dioxide attachment to the host clusters, its reduction to O and CO, and to the complete dissociation, it was found that the total spin magnetic moments of the lowest energy states of the isomers are often quenched with respect to those of initial reagents Fe n +CO 2 . Dissociation pathways of the Fe 2 +CO 2 , Fe 4 +CO 2 , and Fe 16 +CO 2 reactions contain several transition states separated by the local minima states; therefore, a natural question is where do the spin flips occur? Since lifetimes of magnetically excited states were shown to be of the order of 100 fs, the search for the CO 2 dissociation pathways was performed under the assumption that magnetic deexcitation may occur at the intermediate local minima. Two dissociation pathways were obtained for each Fe n +CO 2 reaction using the gradient-based methods. It was found that the Fe 2 +CO 2 reaction is endothermic with respect to both reduction and complete dissociation of CO 2 , whereas the Fe 4 +CO 2 and Fe 16 +CO 2 reactions are exothermic to both reduction and complete dissociation of carbon dioxide. Finally, the CO 2 reduction was found to be more favorable than its complete dissociation in the Fe 4 case.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗