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NASA NTRS1997

Dimerization in Highly Concentrated Solutions of Phosphoimidazolide Activated Mononucleotides

Phosphoimidazolide activated ribomononucleotides (*pN) are useful substrates for the non-enzymatic synthesis of polynucleotides. However, dilute neutral aqueous solutions of *pN typically yield small amounts of dimers and traces of polymers; most of *pN hydrolyzes to yield nucleoside 5'-monophosphate. Here we report the self-condensation of nucleoside 5'-phosphate 2- methylimidazolide (2-MeImpN with N = cytidine, uridine or guanosine) in the presence of Mg2(+) in concentrated solutions, such as might have been found in an evaporating lagoon on prebiotic Earth. The product distribution indicates that oligomerization is favored at the expense of hydrolysis. At 1.0 M, 2-MelmpU and 2-MelmpC produce about 65% of oligomers including 4% of the 3',5'-Iinked dimer. Examination of the product distribution of the three isomeric dimers in a self-condensation allows identification of reaction pathways that lead to dimer formation. Condensations in a concentrated mixture of all three nucleotides (U,C,G mixtures) is made possible by the enhanced solubility of 2-MeImpG in such mixtures. Although percent yield of intemucleotide linked dimers is enhanced as a function of initial monomer concentration, pyrophosphate dimer yields remain practically unchanged at about 20% for 2-MelmpU, 16% for 2-MeImpC and 25% of the total pyrophosphate in the U,C,G mixtures. The efficiency by which oligomers are produced in these concentrated solutions makes the evaporating lagoon scenario a potentially interesting medium for the prebiotic synthesis of dimers and short RNAs.

Kanavarioti, Anastassia↗

DOE OSTI2023

Molecular recognition requires dimerization of a VHH antibody

Camelid heavy-chain-only antibodies are a unique class of antibody that possesses only a single variable domain (termed VHH) for antigen recognition. Despite their apparent canonical mechanism of target recognition, where a single VHH domain binds a single target, an anti-caffeine VHH has been observed to possess 2:1 stoichiometry. Here, the structure of the anti-caffeine VHH/caffeine complex enabled the generation and biophysical analysis of variants that were used to better understand the role of VHH homodimerization in caffeine recognition. VHH interface mutants and caffeine analogs, which were examined to probe the mechanism of caffeine binding, suggested caffeine recognition is only possible with the VHH dimer species. Correspondingly, in the absence of caffeine, the anti-caffeine VHH was found to form a dimer with a dimerization constant comparable to that observed with VH:VL domains in conventional antibody systems, which was most stable near physiological temperature. While the VHH:VHH dimer structure (at 1.13 Å resolution) is reminiscent of conventional VH:VL heterodimers, the homodimeric VHH possesses a smaller angle of domain interaction, as well as a larger amount of apolar surface area burial. To test the general hypothesis that the short complementarity-determining region-3 (CDR3) may help drive VHH:VHH homodimerization, an anti-picloram VHH domain containing a short CDR3 was generated and characterized, which revealed it also existed as dimer species in solution. These results suggest homodimer-driven recognition may represent a more common method of VHH ligand recognition, opening opportunities for novel VHH homodimer affinity reagents and helping to guide their use in chemically induced dimerization applications.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Cleavage at the nsp5–nsp6 site of SARS-CoV-2 main protease intermediate precursor is faster from a monomer than a dimer form

Our previous studies of severe acute respiratory syndrome coronavirus 2 main protease (MPro) precursor monomer indicate that the initial N-terminal nonstructural protein (nsp)4/nsp5 cleavage occurs intramolecularly, with a small fraction of the active site loop equilibrium being in the active state. To understand the influence of dimer formation of MPro upon N-terminal cleavage on the subsequent C-terminal nsp5/nsp6 intermolecular cleavage kinetics, the stepwise processing of a monomeric, inactive precursor containing the native terminal cleavage sites of MPro (MBP- (−6) MPro C145A(+3) -GB1-6H, 86.2 kDa) by mature WT MPro (MPro WT ) was investigated. Differential scanning fluorimetry and analytical ultracentrifugation measurements of various MPro constructs suggest that the C145A mutation decreases the dimer dissociation constant (K dimer ) by ∼26-fold, relative to WT C145 and H41A. The monomeric precursor’s nsp4–nsp5 site appears to saturate MProWT’s active sites and cleave faster, followed by a slower first-order cleavage at the C-terminal site. No detectable product resulting from the C-terminal cleavage is observed until most of the N-terminal cleavage is complete. The initial intermediate product (termed MPro C145A-IP ) is a homodimer with an estimated K dimer of <0.05 μM. In contrast, the first-order kinetics observed for the cleavage of the monomeric form of the intermediate product is at least 300 times faster than that of the dimer form. Room-temperature X-ray structure of the MPro C145A-IP –ensitrelvir complex is like that of the MPro WT –ensitrelvir complex and reveals a dynamic C-terminal region including MPro residues 302 to 306. These results are interpreted from the point of view of a mechanism in which nsp5–nsp6 cleavage may occur from a monomeric intermediate, and dimer formation restricts this cleavage.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Visualizing the Active Site Oxyanion Loop Transition Upon Ensitrelvir Binding and Transient Dimerization of SARS-CoV-2 Main Protease

N-terminal autoprocessing from its polyprotein precursor enables creating the mature-like stable dimer interface of SARS-CoV-2 main protease (MPro), concomitant with the active site oxyanion loop equilibrium transitioning to the active conformation (E*) and onset of catalytic activity. Here, through mutagenesis of critical interface residues and evaluating noncovalent inhibitor (ensitrelvir, ESV) facilitated dimerization through its binding to MPro, we demonstrate that residues extending from Ser1 through Glu14 are critical for dimerization. Combined mutations G11A, E290A and R298A (MPro™) restrict dimerization even upon binding of ESV to monomeric MPro™ with an inhibitor dissociation constant of 7.4 ± 1.6 µM. Contrasting the covalent inhibitor NMV or GC373 binding to monomeric MPro, ESV binding enabled capturing the transition of the oxyanion loop conformations in the absence of a reactive warhead and independent of dimerization. Characterization of complexes by room-temperature X-ray crystallography reveals ESV bound to the E* state of monomeric MPro as well as an intermediate approaching the inactive state (E). It appears that the E* to E equilibrium shift occurs initially from G138-F140 residues, leading to the unwinding of the loop and formation of the 3 10 -helix. Finally, we describe a transient dimer structure of the MPro precursor held together through interactions of residues A5-G11 with distinct states of the active sites, E and E*, likely representing an intermediate in the autoprocessing pathway.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Efficient Intermolecular Charge Transport in π-Stacked Pyridinium Dimers Using Cucurbit[8]uril Supramolecular Complexes

Intermolecular charge transport through π-conjugated molecules plays an essential role in biochemical redox processes and energy storage applications. In this work, we observe highly efficient intermolecular charge transport upon dimerization of pyridinium molecules in the cavity of a synthetic host (cucurbit[8]uril, CB[8]). Stable, homoternary complexes are formed between pyridinium molecules and CB[8] with high binding affinity, resulting in an offset stacked geometry of two pyridiniums inside the host cavity. The charge transport properties of free and dimerized pyridiniums are characterized using a scanning tunneling microscope-break junction (STM-BJ) technique. Our results show that π-stacked pyridinium dimers exhibit comparable molecular conductance to isolated, single pyridinium molecules, despite a longer transport pathway and a switch from intra- to intermolecular charge transport. Control experiments using a CB[8] homologue (cucurbit[7]uril, CB[7]) show that the synthetic host primarily serves to facilitate dimer formation and plays a minimal role on molecular conductance. Molecular modeling using density functional theory (DFT) reveals that pyridinium molecules are planarized upon dimerization inside the host cavity, which facilitates charge transport. In addition, the π-stacked pyridinium dimers possess large intermolecular LUMO–LUMO couplings, leading to enhanced intermolecular charge transport. Altogether, this work demonstrates that supramolecular assembly can be used to control intermolecular charge transport in π-stacked molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Ab initio molecular dynamics free energy study of enhanced copper (II) dimerization on mineral surfaces

Understanding the adsorption of isolated metal cations from water on to mineral surfaces is critical for toxic waste retention and cleanup in the environment. Heterogeneous nucleation of metal oxyhydroxides and other minerals on material surfaces is key to crystal growth and dissolution. The link connecting these two areas, namely cation dimerization and polymerization, is far less understood. In this work we apply ab initio molecular dynamics calculations to examine the coordination structure of hydroxide-bridged Cu(II) dimers, and the free energy changes associated with Cu(II) dimerization on silica surfaces. The dimer dissociation pathway involves sequential breaking of two Cu 2+ -OH – bonds, yielding three local minima in the free energy profiles associated with 0-2 OH – bridges between the metal cations, and requires the design of a (to our knowledge) novel reaction coordinate for the simulations. Cu(II) adsorbed on silica surfaces are found to exhibit stronger tendency towards dimerization than when residing in water. Cluster-plus-implicit-solvent methods yield incorrect trends if OH – hydration is not correctly depicted. The predicted free energy landscapes are consistent with fast equilibrium times (seconds) among adsorbed structures, and favor Cu 2+ dimer formation on silica surfaces over monomer adsorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies

Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Synthesis of (oxo)chlorin dimers chelated with thallium(III)

Two target dimers have been prepared for fundamental studies of hole/electron transfer. Metalation with thallium(III) enables clocking of the rate of hole/electron transfer between the two macrocycles. Each dimer contains a diphenylethyne linker joining two identical hydroporphyrins (chlorin or oxochlorin). The linker is substituted at the 4,4′-positions whereas each (oxo)chlorin is joined at the 10-position. Each (oxo)chlorin is equipped with a gem-dimethyl group at the 18-position to stabilize the hydroporphyrin chromophore toward adventitious dehydrogenation and a 3,5-di-tert-butyl group at the 5-position to achieve increased solubilization in organic media. The dimers parallel a prior set of diphenylethyne-linked (oxo)chlorin constructs containing zinc-free base, zinc-zinc, and copper-copper metalation states that have been examined in studies of electronic communication. The building block (oxo)chlorins for preparing the thallium-containing dimers have been prepared in quantities of 32–404 mg, a scale up to 14-fold larger than previously. Thallation of the free base (oxo)chlorin dimers was achieved with excess TlCl 3 ⋅4H 2 O in CH 2 Cl 2 /CH 3 OH (3–4:1) upon overnight reaction at room temperature. The long-wavelength (Q[Formula: see text] absorption band of (oxo)chlorins lies between that of the zinc(II) and free base counterparts. Absorption spectral comparisons are provided of the thallium(III) and free base (oxo)chlorin monomers and dimers.

Chemistry↗

DOE OSTI2022

Symmetry Breaking Charge Transfer in DNA-Templated Perylene Dimer Aggregates

Molecular aggregates are of interest to a broad range of fields including light harvesting, organic optoelectronics, and nanoscale computing. In molecular aggregates, nonradiative decay pathways may emerge that were not present in the constituent molecules. Such nonradiative decay pathways may include singlet fission, excimer relaxation, and symmetry-breaking charge transfer. Singlet fission, sometimes referred to as excitation multiplication, is of great interest to the fields of energy conversion and quantum information. For example, endothermic singlet fission, which avoids energy loss, has been observed in covalently bound, linear perylene trimers and tetramers. In this work, the electronic structure and excited-state dynamics of dimers of a perylene derivative templated using DNA were investigated. Specifically, DNA Holliday junctions were used to template the aggregation of two perylene molecules covalently linked to a modified uracil nucleobase through an ethynyl group. The perylenes were templated in the form of monomer, transverse dimer, and adjacent dimer configurations. The electronic structure of the perylene monomers and dimers were characterized via steady-state absorption and fluorescence spectroscopy. Initial insights into their excited-state dynamics were gleaned from relative fluorescence intensity measurements, which indicated that a new nonradiative decay pathway emerges in the dimers. Femtosecond visible transient absorption spectroscopy was subsequently used to elucidate the excited-state dynamics. A new excited-state absorption feature grows in on the tens of picosecond timescale in the dimers, which is attributed to the formation of perylene anions and cations resulting from symmetry-breaking charge transfer. Given the close proximity required for symmetry-breaking charge transfer, the results shed promising light on the prospect of singlet fission in DNA-templated molecular aggregates.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

Monomer and dimer structures of cytochrome bo 3 ubiquinol oxidase from Escherichia coli

Abstract The Escherichia coli cytochrome bo 3 ubiquinol oxidase is a four‐subunit heme‐copper oxidase that serves as a proton pump in the E. coli aerobic respiratory chain. Despite many mechanistic studies, it is unclear whether this ubiquinol oxidase functions as a monomer, or as a dimer in a manner similar to its eukaryotic counterparts—the mitochondrial electron transport complexes. In this study, we determined the monomeric and dimeric structures of the E. coli cytochrome bo 3 ubiquinol oxidase reconstituted in amphipol by cryogenic electron microscopy single particle reconstruction (cryo‐EM SPR) to a resolution of 3.15 and 3.46 Å, respectively. We have discovered that the protein can form a dimer with C2 symmetry, with the dimerization interface maintained by interactions between the subunit II of one monomer and the subunit IV of the other monomer. Moreover, the dimerization does not induce significant structural changes in the monomers, except the movement of a loop in subunit IV (residues 67–74).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Impact of Linker Engineering in Core‐Linked Dimeric Acceptors for High‐Performance Organic Solar Cells

Abstract The dimerization of small molecule acceptors (SMAs) is a promising strategy for enhancing the long‐term stability and power conversion efficiency (PCE) of organic solar cells (OSCs). However, the reported DSMAs are primarily limited to end‐linked molecular configurations, highlighting the need for further exploration of various dimer architectures. Herein, the development of two distinct core‐linked dimerized SMAs (DYF‐V and DYF‐E) are reported with tailored linker structures (vinylene and ethynyl, respectively), achieving high‐performance OSCs (PCE = 18.53%). Interestingly, a subtle change in the linker structures results in markedly different molecular properties and photovoltaic performances of the dimer acceptors. DYF‐E with an ethynyl linker exhibits more twisted backbone conformation and mitigated aggregation property compared to DYF‐V, inducing desirable blend morphologies with a polymer donor including high crystallinity, face‐on oriented packing structures, and well‐intermixed domains. Thus, the DYF‐E‐based OSCs exhibit a high PCE (17.02%), which significantly outperforms the DYF‐V‐based OSCs (PCE = 9.98%). Furthermore, the ternary OSCs based on DYF‐E achieve a higher PCE of 18.53%. Thus, this study highlights the significance of selecting an appropriate linker in core‐linked dimerized SMAs for producing high‐performance OSCs.

Oh, Shinbee↗

DOE OSTI2021

First-Principles Predictions of Out-of-Plane Group IV and V Dimers as High-Symmetry, High-Spin Defects in Hexagonal Boron Nitride

Hexagonal boron nitride (h-BN) has been recently found to host a variety of quantum point defects, which are promising candidates as single-photon sources for solid-state quantum nanophotonic applications. Most recently, optically addressable spin qubits in h-BN have been the focus of intensive research due to their unique potential in quantum computation, communication, and sensing. However, the number of high-symmetry, high-spin defects that are desirable for developing spin qubits in h-BN is highly limited. Here, we combine density functional theory (DFT) and quantum embedding theories to show that out-of-plane X N Y i dimer defects (X, Y = C, N, P, and Si) form a new class of stable C 3v spin-triplet defects in h-BN. We find that the dimer defects have a robust 3 A 2 ground state and 3 E excited state, both of which are isolated from the h-BN bulk states. We show that 1 E and 1 A shelving states exist and they are positioned between the 3 E and 3 A 2 states for all the dimer defects considered in this study. To support future experimental identification of the X N Y i dimer defects, we provide extensive characterization of the defects in terms of their spin and optical properties. We predict that the zero-phonon line of the spin-triplet X N Y i defects lies in the visible range (800 nm to 500 nm). We compute the zero-field splitting of the dimers’ spin to range from 1.79 GHz (Si N P i o ) to 29.5 GHz (C N N i o ). Furthermore, our results broaden the scope of high-spin defect candidates that would be useful for the development of spin-based solid-state quantum technologies in two-dimensional hexagonal boron nitride.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Unconventional bipartite entanglement in the quantum dimer magnet Yb2Be 2 SiO 7

The quantum dimer magnet, with antiferromagnetic intradimer and interdimer Heisenberg exchange between spin-1/2 moments, is known to host an (|$\uparrow$$\downarrow$$\rangle$ - |$\downarrow$$\uparrow$$\rangle$)/$\sqrt{2}$ singlet ground state when the intradimer exchange is dominant. Rare-earth-based quantum dimer systems with strong spin-orbit coupling offer the opportunity for tuning their magnetic properties by using magnetic anisotropy as a control knob. Here, we present bulk characterization and neutron scattering measurements of the quantum dimer magnet Yb 2 Be 2 SiO 7 . We find that the Yb3+ ions can be described by an effective spin-1/2 model at low temperatures and the system does not show signs of magnetic order down to 50 mK. The magnetization, heat capacity, and neutron spectroscopy data can be well-described by an isolated dimer model with highly anisotropic exchange that stabilizes a singlet ground state with a wavefunction (|$\uparrow$$\uparrow$$\rangle$ - |$\downarrow$$\downarrow$$\rangle$)/$\sqrt{2}$ or (|$\uparrow$$\uparrow$$\rangle$ + |$\downarrow$$\downarrow$$\rangle$)/$\sqrt{2}$. Our results show that strong spin-orbit coupling can induce unusual entangled states of matter in quantum dimer magnets.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Enhanced rare-earth separation with a metal-sensitive lanmodulin dimer

Technologically critical rare-earth elements are notoriously difficult to separate, owing to their subtle differences in ionic radius and coordination number. The natural lanthanide-binding protein lanmodulin (LanM) is a sustainable alternative to conventional solvent-extraction-based separation. Here we characterize a new LanM, from Hansschlegelia quercus (Hans-LanM), with an oligomeric state sensitive to rare-earth ionic radius, the lanthanum(III)-induced dimer being >100-fold tighter than the dysprosium(III)-induced dimer. X-ray crystal structures illustrate how picometre-scale differences in radius between lanthanum(III) and dysprosium(III) are propagated to Hans-LanM’s quaternary structure through a carboxylate shift that rearranges a second-sphere hydrogen-bonding network. Comparison to the prototypal LanM from Methylorubrum extorquens reveals distinct metal coordination strategies, rationalizing Hans-LanM’s greater selectivity within the rare-earth elements. Finally, structure-guided mutagenesis of a key residue at the Hans-LanM dimer interface modulates dimerization in solution and enables single-stage, column-based separation of a neodymium(III)/dysprosium(III) mixture to >98% individual element purities. This work showcases the natural diversity of selective lanthanide recognition motifs, and it reveals rare-earth-sensitive dimerization as a biological principle by which to tune the performance of biomolecule-based separation processes.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Plasmon-induced excitation energy transfer in silver nanoparticle dimers: A real-time TDDFTB investigation

Here, using real-time quantum dynamics calculations, we perform theoretical investigations of light-induced interactions and electronic excitation transfer in a silver nanoparticle dimer. Real-time time-dependent density functional tight-binding (RT-TDDFTB) calculations provide details of the quantum dynamical processes at an electronic/atomistic level with attosecond resolution. The computational efficiency of RT-TDDFTB allows us to examine electronic dynamics up to picosecond time scales. With time scales varying over six orders of magnitude, we provide insight into interactions between the nanoparticle and laser and between nanoparticles. Our results show that the coupling between nanoparticle monomers is dependent on the separation distance between the nanoparticles in the dimer. As the interparticle distance is varied, the dipole–dipole interactions and electronic excitation transfer mechanisms are markedly different. At large distances (from 50 to 20 Å), the energy transfer from NP1 to NP2 becomes more efficient as the interparticle distance decreases. The total dipole moment of the Ag 14 nanoparticle dimer increases linearly at an interparticle distance of 20 Å and reaches its maximum after 1.2 ps. The electronic excitation transfer is also the most efficient at 20 Å. At short distances, back-transfer effects reduce the ability of the dimer and NP1 to accept energy from the incident electric field. We attribute the distance-dependent features of the nanoparticle dimer to the beating between the laser acting on NP1 and the back transfer from NP2 to NP1.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Harvesting electrons and holes from photodriven symmetry-breaking charge separation within a perylenediimide photosynthetic model dimer

Understanding how to utilize symmetry-breaking charge separation (SB-CS) offers a path toward increasingly efficient light-harvesting technologies. This process plays a central role in the first step of photosynthesis, in which the dimeric “special pair” of the photosynthetic reaction center enters a coherent SB-CS state after photoexcitation. Previous research on SB-CS in both biological and synthetic chromophore dimers has focused on increasing the efficiency of light-driven processes. In a chromophore dimer undergoing SB-CS, the energy of the radical ion pair product is nearly isoenergetic with that of the lowest excited singlet (S 1 ) state of the dimer. This means that very little energy is lost from the absorbed photon. In principle, the relatively high energy electron and hole generated by SB-CS within the chromophore dimer can each be transferred to adjacent charge acceptors to extend the lifetime of the electron–hole pair, which can increase the efficiency of solar energy conversion. To investigate this possibility, we have designed a bis-perylenediimide cyclophane (mPDI 2 ) covalently linked to a secondary electron donor, peri-xanthenoxanthene (PXX) and a secondary electron acceptor, partially fluorinated naphthalenediimide (FNDI). Upon selective photoexcitation of mPDI 2 , transient absorption spectroscopy shows that mPDI 2 undergoes SB-CS, followed by two secondary charge transfer reactions to generate a PXX •+ -mPDI 2 -FNDI •– radical ion pair having a nearly 3 µs lifetime. In conclusion, this strategy has the potential to increase the efficiency of molecular systems for artificial photosynthesis and photovoltaics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers

The sugar-binding receptors dectin-2 and blood dendritic cell antigen 2 (BDCA-2) bind oligosaccharide ligands through extracellular carbohydrate-recognition domains (CRDs) and initiate intracellular signaling through Fc receptor γ adapters (FcRγ). Dectin-2 stimulates macrophages in response to pathogen binding while BDCA-2 modulates cytokine production in plasmacytoid dendritic cells. The oligomeric states of these receptors and the orientations of their CRDs have been investigated by analysis of a naturally occurring disulfide-bonded variant of BDCA-2 and by replacement of transmembrane domains with N-terminal dimerization domains to create extracellular domain dimers of both dectin-2 and BDCA-2. Analysis of these constructs, as well as previously described crystal structures of the CRDs from these proteins and a novel structure of an extended version of the extracellular domain of dectin-2, showed that there is only limited interaction of the CRDs in the dimers, but interactions can be stabilized by the presence of the neck region. The resulting orientation of sugar-binding sites in the dimers would favor crosslinking of multiple dimers by oligosaccharide ligands, causing clustering of FcRγ to initiate signaling.

carbohydrate-binding protein↗

DOE OSTI2022

Interpretation of Ir L-edge isotropic x-ray absorption spectra across the pressure-induced dimerization transition in hyper-honeycomb beta-Li2IrO3

The extended nature of atomic 5d orbitals, together with a relatively short ~ 3 °A Ir-Ir distance across edge-shared octahedra in honeycomb iridate lattices, leads to a tendency to disrupt the local, spin-orbit entangled jeff = 1 2 moments of Ir4+ ions in favor of dimerization and formation of molecular orbitals, especially upon lattice compression. The sensitivity of Ir L-edge spectroscopy to both spin-orbit entanglement in jeff states and quenching of orbital degrees of freedom in dimerized states, results in a peculiar evolution of x-ray absorption spectra across dimerization transitions including energy shifts in opposite direction for L3 and L2 leading absorption edges, and substantial changes in their isotropic branching ratio. We present a theoretical description of the evolution of 5d electronic states, and related x-ray absorption spectra, in going from the single ion to the dimerized limit. The calculations reproduce the experimental results for hyper-honeycomb β-Li2IrO3[1, 2] and shed light into the weakening of the coupling between spin and orbital degrees of freedom as the strength of dimerization increases. The results provide a basis for interpretation of L-edge xray absorption spectra in 5d systems where competition between formation of local jeff states and molecular orbitals is at play.

van Veenendaal, Michel↗