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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
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═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 OSTI2020

Dimer interaction in the Hv1 proton channel

The voltage-gated proton channel Hv1 is a member of the voltage-gated ion channel superfamily, which stands out in design: It is a dimer of two voltage-sensing domains (VSDs), each containing a pore pathway, a voltage sensor (S4), and a gate (S1) and forming its own ion channel. Opening of the two channels in the dimer is cooperative. Part of the cooperativity is due to association between coiled-coil domains that extend intracellularly from the S4s. Interactions between the transmembrane portions of the subunits may also contribute, but the nature of transmembrane packing is unclear. Using functional analysis of a mutagenesis scan, biochemistry, and modeling, we find that the subunits form a dimer interface along the entire length of S1, and also have intersubunit contacts between S1 and S4. These interactions exert a strong effect on gating, in particular on the stability of the open state. Our results suggest that gating in Hv1 is tuned by extensive VSD–VSD interactions between the gates and voltage sensors of the dimeric channel.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2020

ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer

The autophagy-initiating human ULK complex consists of the kinase ULK1/2, FIP200, ATG13, and ATG101. Hydrogen-deuterium exchange mass spectrometry was used to map their mutual interactions. The N-terminal 640 residues (NTD) of FIP200 interact with the C-terminal IDR of ATG13. Mutations in these regions abolish their interaction. Negative stain EM and multiangle light scattering showed that FIP200 is a dimer, while a single molecule each of the other subunits is present. The FIP200NTD is flexible in the absence of ATG13, but in its presence adopts the shape of the letter C ~20 nm across. The ULK1 EAT domain interacts loosely with the NTD dimer, while the ATG13:ATG101 HORMA dimer does not contact the NTD. Cryo-EM of the NTD dimer revealed a structural similarity to the scaffold domain of TBK1, suggesting an evolutionary similarity between the autophagy-initiating TBK1 kinase and the ULK1 kinase complex.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2020

Tracing inter-Coulombic decay of molecular dimers

We have conducted an experimental study on the photo double ionization (PDI) of carbon dioxide dimers and oxygen dimers, while focusing on the dissociation dynamics upon single photon absorption. The results in terms of the kinetic energy and angular distributions of the charged particles show unambiguous experimental evidence of intermolecular Coulombic decay (ICD) in carbon dioxide dimers. In the oxygen dimer, the results show that ICD is accompanied by knock-off ionization mechanisms.

74 ATOMIC AND MOLECULAR PHYSICS↗
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 OSTI2020

Experimental observation of magnetic dimers in diluted Yb:YAlO 3

In this paper, we present a comprehensive experimental investigation of Yb magnetic dimers in Yb 0.04 Y 0.96 AlO 3 , an Yb-doped yttrium aluminum perovskite YAlO3, by means of specific heat, magnetization, and high-resolution inelastic neutron scattering (INS) measurements. In our sample, the Yb ions are randomly distributed over the lattice and ~7% of Yb ions form quantum dimers due to nearest-neighbor antiferromagnetic coupling along the c axis. At zero field, the dimer formation manifests itself in an appearance of an inelastic peak at Δ ≈ 0.2 meV in the INS spectrum and a Schottky-like anomaly in the specific heat. The structure factor of the INS peak exhibits a cosine modulation along the $L$ direction, in agreement with the $c$-axis nearest-neighbor intradimer coupling. A careful fitting of the low-temperature specific heat shows that the excited state is a degenerate triplet, which indicates a surprisingly small anisotropy of the effective Yb-Yb exchange interaction despite the low crystal symmetry and anisotropic magnetic dipole contribution, in agreement with previous reports for the Yb parent compound, YbAlO 3 , and in contrast to Yb 2 Pt 2 Pb. The obtained results are precisely reproduced by analytical calculations for the Yb dimers.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Coupled dimer and bond-order-wave order in the quarter-filled one-dimensional Kondo lattice model

Motivated by experiments on the organic compound (Per) 2 [Pt(mnt) 2 ], we study the ground state of the onedimensional Kondo lattice model at quarter filling with the density matrix renormalization group method. Here, we show a coupled dimer and bond-order-wave (BOW) state in the weak-coupling regime for the localized spins and itinerant electrons, respectively. The quantum phase transitions for the dimer and the BOW orders occur at the same critical coupling parameter J c , with the opening of a charge gap. The emergence of the combination of dimer and BOW order agrees with the experimental findings of the simultaneous Peierls and spin-Peierls transitions at low temperatures, which provides a theoretical understanding of such a phase transition. We also show that the localized spins in this insulating state have quasi-long-ranged spin correlations with collinear configurations, which resemble the classical dimer order in the absence of a magnetic order.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
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 OSTI2020

Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize

Interactions between MADS-box transcription factors are critical in the regulation of floral development, and shifting MADS-box protein-protein interactions are predicted to have influenced floral evolution. However, precisely how evolutionary variation in protein-protein interactions affects MADS-box protein function remains unknown. To assess the impact of changing MADS-box protein-protein interactions on transcription factor function, we turned to the grasses, where interactions between B-class MADS-box proteins vary. We tested the functional consequences of this evolutionary variability using maize as an experimental system. We found that differential B-class dimerization was associated with subtle, quantitative differences in stamen shape. In contrast, differential dimerization resulted in large-scale changes to downstream gene expression. Differential dimerization also affected B-class complex composition and abundance, independent of transcript levels. This indicates that differential B-class dimerization affects protein degradation, revealing an important consequence for evolutionary variability in MADS-box interactions. Our results highlight complexity in the evolution of developmental gene networks - changing protein-protein interactions could affect not only the composition of transcription factor complexes, but also their degradation and persistence in developing flowers. Here, our results also show how coding change in a pleiotropic master regulator could have small, quantitative effects on development.

59 BASIC BIOLOGICAL SCIENCES↗
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.↗
NASA NTRS1992

A molecular beam mass spectrometric study of the formation and photolysis of C(lc)lO dimer

A study of the chlorine oxides present at temperatures and pressures typical of the Antarctic stratosphere was carried out. A series of low temperature flow reactors was constructed and used in conjunction with molecular beam mass spectrometric techniques to identify species and characterize their kinetic behavior at temperatures of -20 to -70 C and pressures of from 30 to 130 Torr. It was found that the gas phase chlorine-oxygen system was quite complex at low temperatures. ClO dimer was identified and found to be thermodynamically very stable under stratospheric conditions. It was also found that any system which contained ClO also contained a larger oxide. The oxide was identified as Cl2O3. A survey of possible higher oxides, which have been postulated as possible chlorine sinks in the stratosphere, was also carried out. The rate of formation of ClO dimer was measured as a function of temperature and pressure. Measurements were made of both the decay of ClO and the formation of the dimer. By comparing these rates it was determined that virtually all of the ClO was converted to the dimer under stratospheric conditions, and that the other ClO reactions were not important under these conditions.

Greene, Frank T.↗
NASA NTRS1995

Reduced dimer production in solar-simulator-pumped continuous wave iodine lasers based on model simulations and scaling and pumping studies

A numerical rate equation model for a continuous wave iodine laser with longitudinally flowing gaseous lasant is validated by approximating two experiments that compare the perfluoroalkyl iodine lasants n-C3F7I and t-C4F9I. The salient feature of the simulations is that the production rate of the dimer (C4F9)2 is reduced by one order of magnitude relative to the dimer (C3F7)2. The model is then used to investigate the kinetic effects of this reduced dimer production, especially how it improves output power. Related parametric and scaling studies are also presented. When dimer production is reduced, more monomer radicals (t-C4F9) are available to combine with iodine ions, thus enhancing depletion of the laser lower level and reducing buildup of the principal quencher, molecular iodine. Fewer iodine molecules result in fewer downward transitions from quenching and more transitions from stimulated emission of lasing photons. Enhanced depletion of the lower level reduces the absorption of lasing photons. The combined result is more lasing photons and proportionally increased output power.

Costen, Robert C.↗