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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2024

Dimer piling problems and interacting field theory

The dimer tiling problem asks in how many ways can the edges of a graph be covered by dimers so that each site is covered once. In the special case of a planar graph, this problem has a solution in terms of a free fermionic field theory. We rediscover and explore an expression for the number of coverings of an arbitrary graph by arbitrary objects in terms of an interacting fermionic field theory first proposed by Samuel. Generalizations of the dimer tiling problem, which we call “dimer piling problems,” demand that each site be covered N times by indistinguishable dimers. Our field theory provides a solution of these problems in the large- N limit. We give a similar path integral representation for certain lattice coloring problems. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
NASA NTRS1973

Condensation in CO2 free jet expansions. I - Dimer formation.

A theoretical and experimental investigation of the kinetics of CO2 dimer formation in the adiabatically expanding core of a free jet expansion has been carried out. The theoretical analysis is based on dimer formation by an efficient termolecular process and dimer destruction by bimolecular collisions. Account is taken of the expected variation of the specific heat ratio during the expansion and of the effective increase in the termolecular collision rate at low temperatures due to the presence of loosely bound orbiting pairs. Experimental dimer concentrations were measured mass spectrometrically by forming a molecular beam from the expanded gas mixture after the onset of molecular flow. Observed dimer concentrations, for a range of pre-expansion conditions of 400 to 900 torr pressure and room temperature, are in good agreement with the theoretical analysis, provided that account is taken of the effect of loosely bound orbiting pairs at low temperatures.

Dorfeld, W. G.↗
NASA NTRS1988

Chemistry of the CO dimer at low temperatures

Researchers conducted a series of experiments on the chlorine-catalyzed photodecomposition of O sub 3 both in the gas and in inert solvents such as CF sub 4 and CO sub 2 in the temperature range about 190 to 225 K. The liquid medium was chosen in order to minimize possible surface loss of long-lived ClO dimer, and to aid in the stabilization of transient excited intermediates. The mechanism of dimer formation was as follows: (1) Cl sub 2 + hv yields Cl + Cl; (2) Cl + O sub 3 yields ClO + O sub 2; (3) ClO + ClO yields Cl sub 2 O sub 2. The experiments were done in cooled low temperature cells, with irradiation from an Osram high pressure mercury arc, filtered to remove radiation below 325 nm. Spectral analysis was by means of a Cary Model 2200 UV spectrometer. The principal objectives were: (1) to determine the lifetime of the dimer as a function of temperature; (2) to observe spectral changes in the mixtures which could be attributed to dimer or related products; and (3) to observe chemical or photochemical reactions of the dimer.

Demore, W. B.↗
DOE OSTI2024

SAXS of murine amelogenin identifies a persistent dimeric species from pH 5.0 to 8.0

Amelogenin is an intrinsically disordered protein essential to tooth enamel formation in mammals. Here, using advanced small angle X-ray scattering (SAXS) capabilities at synchrotrons and computational models, we revisited measuring the quaternary structure of murine amelogenin as a function of pH and phosphorylation at serine-16. The SAXS data shows that at the pH extremes, amelogenin exists as an extended monomer at pH 3.0 (R g = 38.4 Å) and nanospheres at pH 8.0 (R g = 84.0 Å), consistent with multiple previous observations. At pH 5.0 and above there was no evidence for a significant population of monomeric species. Instead, at pH 5.0 ~ 80% of the population is a heterogenous dimeric species that increases to ~ 100% at pH 5.5. The dimer population was observed at all pH > 5 conditions in dynamic equilibrium with a species in the pentamer range at pH < 6.5 and nanospheres at pH 8.0. At pH 8.0 ~ 40% of the amelogenin still remained in the dimeric state. In general, serine-16 phosphorylation of amelogenin appears to modestly stabilize the population of the dimeric species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Modeling Surface-Enhanced Raman Scattering of Au-Pyrazine and Au-Pyrazine-Au Nanorod Dimer Systems with the TD-DFTB Method

This study investigates Raman scattering from a pyrazine molecule adsorbed on gold nanorod surfaces using the time-dependent density functional tight-binding (TD-DFTB) method. We analyze surface enhanced Raman scattering (SERS) of the molecule for two configurations: one where the molecule is adsorbed on a single gold nanorod forming Au-pyrazine complex, and another where it forms a nano-junction Au-pyrazine-Au dimer system. These two configurations offer distinct chemical environments for the molecule and different local field enhancements, with the dimer systems generating enhanced hotspot regions at the junctions. We present results for nanojunction, Au-pyrazine-Au dimer structures, for variable nanogap sizes that lead to shift in the plasmon energy. The study identifies contributions to the SERS enhancements from chemical, electromagnetic, and resonance charge transfer mechanisms. Our results show that the chemical mechanism provides enhancement factors in the range of 10 2 –10 3 , while the electromagnetic enhancements are on the order of 10 3 –10 5 for monomer systems and 10 6 –10 8 for dimer structures. We present results for a nanorod with a length of 5.3 nm and a width of 0.52 nm, consisting of 121 gold atoms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Characterizing Ultrafast Intersystem Crossing Pathways in Molecular Pt Dimers Using Time-Resolved Wide-Angle X-ray Scattering

Vibronic coupling between transition metal charge transfer states is a potential mechanism for enhancing the intersystem crossing (ISC) rate. Vibronic coupling-driven ISC has been observed in Pt­(II) dimer complexes, where the trajectory across excited-state pathways is tuned by atomic displacements via Pt–Pt stretching vibrations. Time-resolved wide-angle X-ray scattering (TR-WAXS) was utilized to quantify the Pt–Pt contraction following metal–metal-to-ligand charge transfer (MMLCT) excitation in Pt dimers with different bridging ligands. Both complexes exhibit Pt–Pt bond formation with a decrease in Pt–Pt distance of ∼ 0.25 Å and coherent vibrational wavepackets (CVWPs) encoded in the Pt–Pt contraction of both dimers. However, the complexes exhibit different time-dependent evolution of their CVWPs. Analysis of interference patterns between different CVWPs is used to track the trajectory across the excited-state surfaces. Furthermore, this work demonstrates that the interference between CVWPs in ultrafast TR-WAXS encodes indirect information regarding electronic excited-states to reveal the Pt dimer bridge-dependent ISC mechanism.

Computational chemistry↗
DOE OSTI2024

Correlation of Dimer-Linker-Induced Conformational Lock with Nonradiative Energy Loss in Organic Solar Cells

The efficiencies of dimer-based devices still lag those of their small molecule-based counterparts. This is primarily due to the considerable dihedrals in the dimer skeleton, which compromises the molecular packing, thus influencing the charge generation and nonradiative voltage loss (ΔV oc,nr ). Herein, we developed two dimeric acceptors with varied π-linkers to investigate the influence of linker-induced conformational lock on ΔV oc,nr . We find that the helically lapped O-shaped dimer delivers better intermolecular packing than the planar S-shaped one that incorporates a bulkier π-linker. However, its planar skeleton is instead more favorable for forming a compact and ordered stacking with the host acceptor in ternary blend. This possibly promotes exciton dissociation, thus reducing the nonradiative decay of excited states. Moreover, its longer exciton lifetime could offer additional charge-transfer channels. Finally, these contributions effectively minimize ΔV oc,nr to 0.195 eV, while delivering a high efficiency approaching 20% in the derived ternary device.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Exchange-biased quantum tunnelling of magnetization in a [Mn 3 ] 2 dimer of single-molecule magnets with rare ferromagnetic inter-Mn 3 coupling

A covalently-linked dimer of two single-molecule magnets (SMMs), [Mn 6 O(O 2 CMe) 6 (1,3-ppmd) 3 ](ClO 4 ) 2 , has been synthesized from the reaction of [Mn 3 O(O 2 CMe) 6 (py) 3 ](ClO 4 ) with 1,3-phenylene-bis(pyridin-2-ylmethanone) dioxime (1,3-ppmdH 2 ). It contains two [Mn III 3 O] +7 triangular units linked by three 1,3-ppmd 2 - groups into an [Mn 3 ] 2 dimer with D 3 symmetry. Solid-state dc and ac magnetic susceptibility measurements showed that each Mn 3 subunit retains its properties as an SMM with an S = 6 ground state. Magnetization vs. dc field sweeps on a single crystal reveal hysteresis loops below 1.3 K exhibiting exchange-biased quantum tunnelling of magnetization (QTM) steps with a bias field of +0.06 T. This is the first example of a dimer of SMMs showing a positive exchange bias of the QTM steps in the hysteresis loops, and it has therefore been subjected to a detailed analysis. Simulation of the loops determines that each Mn3 unit is exchange-coupled with its neighbour primarily through the 1,3-ppmd 2 - linkers, confirming a weak ferromagnetic inter-Mn 3 interaction of J 12 ≈ +6.5 mK ($\hat{H}= -2J\hat{S}_i·\hat{S}_j$ convention). High-frequency EPR studies of a microcrystalline powder sample enable accurate determination of the zero-field splitting parameters of the uncoupled Mn3 SMMs, while also confirming the weak exchange interaction between the two SMMs within each [Mn 3 ] 2 dimer. The combined results emphasize the ability of designed covalent linkers to generate inter-SMM coupling of a particular sign and relative magnitude, and thus the ability of such linkers to modulate the quantum physics. As such, this article supports the feasibility of using designed covalent linkers to develop molecular oligomers of SMMs, or other magnetic molecules, as multi-qubit systems and/or other components of new quantum technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

A novel symmetric pyrazine (pyz)-bridged uranyl dimer [UO 2 Cl 3 (H 2 O)(Pyz) 0.5 ] 2 2– : synthesis, structure and computational analysis

In this work, we report on the synthesis of (HPyz + ) 2 [UO 2 Cl 3 (H 2 O)(Pyz) 0.5 ] 2 ·2H 2 O which features a novel pyrazine-bridged uranyl dimer, [UO 2 Cl 3 (H 2 O)(Pyz) 0.5 ] 2 2– . A rigorous computational and experimental analysis of this compound was performed to fully explore the influence of coordination on the electronic structure and potential charge-transfer characteristics of this dimer, revealing a delocalized π-system across the bridging pyrazine and the axial components of both uranyl centers. Electrostatic surface potentials, used to rationalize the observed assembly, indicate a decreased basicity of the uranyl oxo versus [UO 2 Cl 4 ] 2– , and signify a lessened capacity for the terminal –yl oxos of the [UO 2 Cl 3 (H 2 O)(Pyz) 0.5 ] 2 2– dimer to participate in supramolecular assembly. A combined density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) analysis further evidenced an increase in U&#x2550;O bond strengths within the dimer, which is supported by a blue shift in the characteristic Raman-active uranyl symmetric stretch (ν 1 ) with respect to the more typically observed [UO 2 Cl 4 ] 2– .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Decorrelated singlet and triplet exciton delocalization in acetylene-bridged Zn-porphyrin dimers

The controlled delocalization of molecular excitons remains an important goal towards the application of organic chromophores in processes ranging from light-initiated chemical transformations to classical and quantum information processing. In this study, we present a methodology to couple optical and magnetic spectroscopic techniques and assess the delocalization of singlet and triplet excitons in model molecular chromophores. By comparing the steady-state and time-resolved optical spectra of Zn-porphyrin monomers and weakly coupled dimers, we show that we can use the identity of substituents bound at specific positions of the macromolecules' rings to control the inter-ring delocalization of singlet excitons stemming from their B states through acetylene bridges. While broadened steady-state absorption spectra suggest the presence of delocalized B state excitons in mesityl-substituted Zn-tetraphenyl porphyrin dimers (Zn 2 U-D), we confirm this conclusion by measuring an enhanced ultrafast non-radiative relaxation from these inter-ring excitonic states to lower lying electronic states relative to their monomer. In contrast to the delocalized nature of singlet excitons, we use time-resolved EPR and ENDOR spectroscopies to show that the triplet states of the Zn-porphyrin dimers remain localized on one of the two macrocyclic sub-units. We use the analysis of EPR and ENDOR measurements on unmetallated model porphyrin monomers and dimers to support this conclusion. The results of DFT calculations also support the interpretation of localized triplet states. These results demonstrate researchers cannot conclude triplet excitons delocalize in macromolecular based on the presence of spatially extended singlet excitons, which can help in the design of chromophores for application in spin conversion and information processing technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Modulating metal-centered dimerization of a lanthanide chaperone protein for separation of light lanthanides

Elucidating details of biology’s selective uptake and trafficking of rare earth elements, particularly the lanthanides, has the potential to inspire sustainable biomolecular separations of these essential metals for myriad modern technologies. Here, we biochemically and structurally characterize Methylobacterium (Methylorubrum) extorquens LanD, a periplasmic protein from a bacterial gene cluster for lanthanide uptake. This protein provides only four ligands at its surface-exposed lanthanide-binding site, allowing for metal-centered protein dimerization that favors the largest lanthanide, La III . However, the monomer prefers Nd III and Sm III , which are disfavored lanthanides for cellular utilization. Structure-guided mutagenesis of a metal-ligand and an outer-sphere residue weakens metal binding to the LanD monomer and enhances dimerization for Pr III and Nd III by 100-fold. Selective dimerization enriches high-value Pr III and Nd III relative to low-value La III and Ce III in an all-aqueous process, achieving higher separation factors than lanmodulins and comparable or better separation factors than common industrial extractants. Finally, we show that LanD interacts with lanmodulin (LanM), a previously characterized periplasmic protein that shares LanD’s preference for Nd III and Sm III . Our results suggest that LanD’s unusual metal-binding site transfers less-desirable lanthanides to LanM to siphon them away from the pathway for cytosolic import. The properties of LanD show how relatively weak chelators can achieve high selectivity, and they form the basis for the design of protein dimers for separation of adjacent lanthanide pairs and other metal ions.

lanthanide biochemistry↗
DOE OSTI2023

Nanoscale imaging of quantum dot dimers using time-resolved super-resolution microscopy combined with scanning electron microscopy

Abstract Time-resolved super-resolution microscopy was used in conjunction with scanning electron microscopy to image individual colloidal CdSe/CdS semiconductor quantum dots (QD) and QD dimers. The photoluminescence (PL) lifetimes, intensities, and structural parameters were acquired with nanometer scale spatial resolution and sub-nanosecond time resolution. The combination of these two techniques was more powerful than either alone, enabling us to resolve the PL properties of individual QDs within QD dimers as they blinked on and off, measure interparticle distances, and identify QDs that may be participating in energy transfer. The localization precision of our optical imaging technique was ∼3 nm, low enough that the emission from individual QDs within the dimers could be spatially resolved. While the majority of QDs within dimers acted as independent emitters, at least one pair of QDs in our study exhibited lifetime and intensity behaviors consistent with resonance energy transfer from a shorter lifetime and lower intensity donor QD to a longer lifetime and higher intensity acceptor QD. For this case, we demonstrate how the combined super-resolution optical imaging and scanning electron microscopy data can be used to characterize the energy transfer rate.

36 MATERIALS SCIENCE↗
DOE OSTI2026

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks

Exonuclease/endonuclease/phosphatase (EEP)-fold hydrolases are canonically monomeric phosphodiesterases exemplified by APE1, DNase I, and TDP2 nucleases. While EEP family domain containing protein 1 (EEPD1) acts in DNA stress responses, its proposed nuclease activities are enigmatic. Here, we integrate hybrid structural methods, evolution, biochemistry, cancer genomics, plus molecular and cell biology to define EEPD1 structure, assembly, and function at stalled DNA replication forks. Results imply EEPD1 surprisingly requires both unique EEP domain dimer and distinctive tandem Helix-hairpin-Helix [(HhH) 2 ] domains to clamp double-stranded (ds) DNA at reversed DNA replication forks for fork protection. Small-angle X-ray Scattering (SAXS), crystal, and cryo-EM structures unveil an unprecedented tryptophan handshake dimer, conserved interface di-Trp-Pro pocket, and adjustable “wrist” enabling an open-closed conformational switch. EEPD1 dimer cooperatively binds complex dsDNA replication fork intermediates but alone lacks nuclease activity due to loss of key EEP catalytic residues during Metazoan evolution and atmospheric oxygen buildup. Instead, EEPD1 prevents nucleolytic degradation of reversed replication forks by MRE11. Furthermore, cancer bioinformatics support oxidative damage-dependent EEPD1 association as a significant modulator of overall patient survival. Collective findings uncover unexpected EEP dimer and fork protection function in clamping, not cleaving, reversed replication forks for metazoan oxidative stress responses controlling genome stability and cancer outcomes.

Shen, Runze [Univ. of Texas, Houston, TX (United S↗
DOE OSTI2025

Localized triplons and site stuffing in the quantum dimer magnet BiYbGeO5

Thermodynamic and muon spin relaxation measurements have recently highlighted BiYbGeO5 as a new example of a rare-earth-based quantum dimer magnet with isolated Yb3+ spin-1/2 dimers. However, direct spectroscopic evidence of the triplet excitations and measurements of the structural disorder are lacking. In this work, polycrystalline BiYbGeO5 was synthesized using conventional high-temperature solid-state methods and investigated via high-resolution neutron powder diffraction and inelastic neutron scattering. Diffraction measurements down to 58 mK reveal no signatures of magnetic order and indicate that nearly 20% of Yb3+ sites are replaced by nonmagnetic Bi3+, introducing significant structural disorder. Inelastic neutron scattering shows dispersionless triplon excitations, consistent with localized, noninteracting spin dimers. Fits to the triplet excitation spectrum with an XXZ-type anisotropic exchange give 𝐽XX=0.100⁢(1)⁢meV and 𝐽Z=0.202⁢(1)⁢meV. These findings establish BiYbGeO5 as a structurally disordered but magnetically well-isolated quantum dimer system, providing a model platform for studying the resilience of entangled spin states to site dilution.

Kapoor, Rachit [Brock University, Canada]↗
DOE OSTI2024

Random singlet-like state in the dimer-based triangular antiferromagnet Ba 6 Y 2 Rh 2 Ti 2 O 17 − δ

We present the magnetic, thermodynamic, and muon spin relaxation ( μ SR ) results of the dimer-based triangular antiferromagnet Ba 6 Y 2 Rh 2 Ti 2 O 17 − δ . The magnetic susceptibility data show the sub-Curie-Weiss behavior χ ( T ) ∝ T − α χ below 100 K, suggesting random magnetism. The isothermal magnetization results reveal the presence of weakly interacting structural orphan spins about 6.1 % at 2 K, arising from the oxygen deficiency. The comprehensive μ SR experiments exhibit the coexisting relaxing and nonrelaxing components along with the thermally activated behavior in the muon spin relaxation rate, reflecting the fluctuating orphan spins in the dimer singlet background. In addition, we observe the scaling behavior of M ( H , T ) in H / T and P z ( t ) in t / H LF with the scaling exponents α χ = α M = 0.75 and α μ = 0.72 , respectively, but not for the magnetic specific heat data. The failure of the scaling relation in C m ( H , T ) / T implies low-energy excitations dressed by the conventional orphan spins. Based on these observations, we find that the magnetic ground state resembles random singlets and discuss the possible configurations of the spin dimer unit Rh 2 O 9 . Our results shed light on the role of quenched disorder in the dimer-based frustrated magnets. Published by the American Physical Society 2024

Lee, Wonjun (ORCID:000000034848852X)↗
DOE OSTI2026

Biochemical parallels between catabolic pathways for lignin-associated aromatic dimers

Lignin is one of the most common biopolymers on Earth. In nature, lignin is primarily deconstructed by fungi into mixtures of aromatic compounds that are then assimilated by bacteria and fungi. Industrially, lignin is primarily generated as a byproduct of pulp and paper production and burned for process heat. However, if the appropriate assimilatory pathways were identified, deconstructed lignin could be funneled into value-added products using engineered bacteria. Foundational work has described pathways for assimilation of diverse monomeric aromatic compounds such as protocatechuate, ferulate, and syringate, as well as select dimers including those with β-O-4 and 5-5 interunit linkages. Recent advances have elucidated additional pathways for dimer assimilation, including pathways for new substrates as well as parallel pathways for previously characterized substrates. Comparing these dimer assimilation pathways can illuminate the underlying biochemical logic of assimilation for lignin-associated aromatic dimers and provide opportunities for metabolic engineering to enhance lignin valorization.

Sphingomonas↗
NASA NTRS1989

Oligomerization of deoxynucleoside-biphosphate dimers - Template and linkage specificity

The oligomerization of the activated 3-prime-5-prime pyrophosphate-linked dimer, pdAppdAp, is presently noted to be selectively favored by a poly(U) template over the 3-prime-3-prime and 5-prime-5-prime linked dimers. Both overall yields and the production of the longest oligomers were markedly stimulated by poly(U)'s presence; in its absence, the 5-prime-5-prime linked dimer became the most reactive, yielding chains of the order of 60 monomer-unit lengths. Remarkable self-organization properties are noted for the 5-prime-5-prime dimer of pdAp.

Visscher, J.↗