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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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

Conformational Panorama and Chirality Controlled Structure–Energy Relationship in a Chiral Carboxylic Acid Dimer

Chirality recognition in dimers of tetrahydro-2-furoic acid (THFA) was studied in a conformer-specific manner using rotational spectroscopy and theoretical approaches. THFA shows a strong preference for the trans- over the cis-COOH configuration. Two drastically different scenarios are possible for the detectable (THFA) 2 : a kinetically preferred dimer bound by feeble interactions between two trans-THFAs or a thermodynamically favored dimer with a double hydrogen-bonded ring structure between two cis subunits. To identify the conformers responsible for the extremely dense rotational spectra observed, it was essential not only to locate several hundred homo/heterochiral (THFA) 2 minima in ab initio calculations but also to evaluate the energetic connectivities among the minima. The study further reveals an interesting chirality dependent structure-energy ordering relationship. A method for enantiomeric excess (ee) determination of THFA is presented using a recently proposed chiral self-tag approach.

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

Metal-organic framework supported single-site nickel catalysts for butene dimerization

Homotopic sites in a well-controlled environment are not only ideal systems for mechanistic studies, but also allow optimal control of catalytic transformations. Sites having only a single metal cation and sites consisting of metal oxo complexes with few nickel (Ni) cations supported on the nodes of UiO-66 metal-organic framework (Ni-UiO-66) are studied for 1-butene dimerization. Monomeric Ni sites, which bind to the Zr 6 node via two Zr-OH(µ3) linkages, are active and selective for the dimerization of 1-butene to linear and mono-branched C 8 isomers. Ni oxo complexes with few Ni cations show lower activity and promote the oligomerization of transiently formed C 8 isomers. In conclusion, Kohn-Sham density function theory calculations combined with spectroscopic measurements and kinetic analyses indicate that dimerization follows a Cossee-Arlman reaction mechanism.

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

Influence of 1-Butene Adsorption on the Dimerization Activity of Single Metal Cations on UiO-66 Nodes

Grafting metal cations to missing linker defect sites in zirconium-based metal–organic frameworks, such as UiO-66, produces a uniquely well-defined and homotopic catalytically active site. We present here the synthesis and characterization of a group of UiO-66-supported metal catalysts, M-UiO-66 (M = Ni, Co, Cu, and Cr), for the catalytic dimerization of alkenes. The hydrogen–deuterium exchange via deuterium oxide adsorption followed by infrared spectroscopy showed that the last molecular water ligand desorbs from the sites after evacuation at 300 °C leading to M(OH)-UiO-66 structures. Adsorption of 1-butene is studied using calorimetry and density functional theory techniques to characterize the interactions of the alkene with metal cation sites that are found active for alkene oligomerization. For the most active Ni-UiO-66, the removal of molecular water from the active site significantly increases the 1-butene adsorption enthalpy and almost doubles the catalytic activity for 1-butene dimerization in comparison to the presence of water ligands. Other M-UiO-66 (M = Co, Cu, and Cr) exhibit 1–3 orders of magnitude lower catalytic activities compared to Ni-UiO-66. The catalytic activities correlate linearly with the Gibbs free energy of 1-butene adsorption. Furthermore, density functional theory calculations probing the Cossee–Arlman mechanism for all metals support the differences in activity, providing a molecular level understanding of the metal site as the active center for 1-butene dimerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Sensor Domain of Histidine Kinase VxrA of Vibrio cholerae : Hairpin-Swapped Dimer and Its Conformational Change

VxrA and VxrB are cognate histidine kinase (HK)-response regulator (RR) pairs of a two-component signaling system (TCS) found in Vibrio cholerae, a bacterial pathogen that causes cholera. The VxrAB TCS positively regulates virulence, the type VI secretion system, biofilm formation, and cell wall homeostasis in V. cholerae, providing protection from environmental stresses and contributing to the transmission and virulence of the pathogen. The VxrA HK has a unique periplasmic sensor domain (SD) and, remarkably, lacks a cytoplasmic linker domain between the second transmembrane helix and the dimerization and histidine phosphotransfer (DHp) domain, indicating that this system may utilize a potentially unique signal sensing and transmission TCS mechanism. Here, we have determined several crystal structures of VxrA-SD and its mutants. These structures reveal a novel structural fold forming an unusual β hairpin-swapped dimer. A conformational change caused by relative rotation of the two monomers in a VxrA-SD dimer could potentially change the association of transmembrane helices and, subsequently, the pairing of cytoplasmic DHp domains. Based on the structural observation, we propose a putative scissor-like closing regulation mechanism for the VxrA HK. IMPORTANCE V. cholerae has a dynamic life cycle, which requires rapid adaptation to changing external conditions. Two-component signal transduction (TCS) systems allow V. cholerae to sense and respond to these environmental changes. The VxrAB TCS positively regulates a number of important V. cholerae phenotypes, including virulence, the type six secretion system, biofilm formation, and cell wall homeostasis. Here, we provide the crystal structures of the VxrA sensor histidine kinase sensing domain and propose a mechanism for signal transduction. The cognate signal for VxrAB remains unknown; however, in this work we couple our structural analysis with functional assessments of key residues to further our understanding of this important TCS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Regiospecific Incorporation of Acetylene Linker in High‐Electron Mobility Dimerized Acceptors for Organic Solar Cells with High Efficiency (18.8%) and Long 1‐Sun Lifetime (> 5000 h)

Abstract The commercialization of organic solar cells (OSCs) requires both high power conversion efficiency (PCE) and long‐term stability. However, the lifetime of the OSCs containing small‐molecule acceptors (SMA) should be significantly enhanced. In this study, a series of planarity‐controlled is developed, high electron mobility dimerized SMAs (DSMAs) and realize OSCs with high‐performance (PCE = 18.8%) and high‐stability ( t 80% lifetime = 5380 h under 1‐Sun illumination). An acetylene linker with a planar triple bond is designed for dimerization of SMA units to afford the high backbone planarity necessary to achieve high crystallinity and electron mobility. To further engineer the molecular conformation and electron mobility of the DSMAs, different regioisomers of a Y‐based SMA are dimerized to yield three regioisomerically distinct DSMAs, denoted as DYA‐I, DYA‐IO, and DYA‐O, respectively. It is found that the crystallinity, electron mobility, and glass transition temperature of the DSMAs gradually increase in the order of DYA‐O, DYA‐IO, and DYA‐I, which, in turn, enhance the PCE and device stability of the resulting OSCs; DYA‐O (PCE = 16.45% and t 80% lifetime = 3337 h) < DYA‐IO (PCE = 17.54% and t 80% lifetime = 4255 h) < DYA‐I (PCE = 18.83% and t 80% lifetime = 5380 h).

Chemistry↗
DOE OSTI2025

Zinc(II) Monomeric, Dimeric, and Trimeric Photosensitizers with Microsecond‐Lived Intra‐ligand Charge Transfer Excited States Investigated through Time‐Resolved Optical and X‐Ray Spectroscopy

Zn II photosensitizers relative to Cu I complexes have received less attention due to their energetically higher metal‐to‐ligand charge transfer states. Three Zn II complexes, namely a Monomer, a bimetallic helicate, and a trimetallic helicate, bearing phenanthroline ligands are hereby studied through time‐resolved X‐ray absorption (tr‐XAS) and femto‐microsecond optical transient absorption spectroscopy (OTA). The formation of intraligand singlet charge transfer ( I ILCT) excited states is achieved within femtoseconds, followed by intersystem crossing (ISC) in nanoseconds to generate microsecond‐lived triplet ( 3 ILCT) states. Femtosecond OTA shows that the 1 ILCT states in the Monomer, Dimer, and Trimer occur within 235 fs, 683 fs, and 730 fs, respectively, while nano‐microsecond OTA and tr‐XAS show their 3 ILCT states to decay within 1.00 µs, 1.48 µs, and 1.51 µs. The ISC from the 1 ILCT to the 3 ILCT state for the Trimer is 42.8 ns compared to the Monomer and Dimer with ISC rates of less than 13 ns. These differences arise due to the stabilization by π‐π and CH‐π noncovalent interactions of the phenanthroline ligands. The dihedral and torsional angles indicate stronger ligand strains in the excited states of the Dimer and Trimer versus the Monomer. DFT calculations for the electrochemical oxidation potentials further highlight their capability in inducing photoredox processes.

earth-abundant Zn-based photosensitizers↗