Search NASA⌕ Search

SEARCH · Search NASA

Results for “dimerization mechanism”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Bond clusters control rupture force limit in shear loaded histidine-Ni 2+ metal-coordinated proteins

Dynamic noncovalent interactions are pivotal to the structure and function of biological proteins and have been used in bioinspired materials for similar roles. Metal-coordination bonds, in particular, are especially tunable and enable control over static and dynamic properties when incorporated into synthetic materials. Despite growing efforts to engineer metal-coordination bonds to produce strong, tough, and self-healing materials, the systematic characterization of the exact contribution of these bonds towards mechanical strength and the effect of geometric arrangements is missing, limiting the full design potential of these bonds. In this work, we engineer the cooperative rupture of metal-coordination bonds to increase the rupture strength of metal-coordinated peptide dimers. Utilizing all-atom steered molecular dynamics simulations on idealized bidentate histidine-Ni 2+ coordinated peptides, we show that histidine-Ni 2+ bonds can rupture cooperatively in groups of two to three bonds. We find that there is a strength limit, where adding additional coordination bonds does not contribute to the additional increase in the protein rupture strength, likely due to the highly heterogeneous rupture behavior exhibited by the coordination bonds. Further, we show that this coordination bond limit is also found natural metal-coordinated biological proteins. Using these insights, we quantitatively suggest how other proteins can be rationally designed with dynamic noncovalent interactions to exhibit cooperative bond breaking behavior. Altogether, this work provides a quantitative analysis of the cooperativity and intrinsic strength limit for metal-coordination bonds with the aim of advancing clear guiding molecular principles for the mechanical design of metal-coordinated materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Local Structure of Glassy Lithium Phosphorus Oxynitride Thin Films: A Combined Experimental and Ab Initio Approach

Lithium phosphorus oxynitride (LiPON) is an amorphous solid–state lithium ion conductor displaying exemplary cyclability against lithium metal anodes. There is no definitive explanation for this stability due to the limited understanding of the structure of LiPON. Herein, we provide a structural model of RF–sputtered LiPON. Information about the short–range structure results from 1D and 2D solid–state NMR experiments. These results are compared with first principles chemical shielding calculations of Li–P–O/N crystals and ab initio molecular dynamics–generated amorphous LiPON models to unequivocally identify the glassy structure as primarily isolated phosphate monomers with N incorporated in both apical and as bridging sites in phosphate dimers. Structural results suggest LiPON's stability is a result of its glassy character. In conclusion, free–standing LiPON films are produced that exhibit a high degree of flexibility, highlighting the unique mechanical properties of glassy materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Rapid Electrochemical Methane Functionalization Involves Pd–Pd Bonded Intermediates

High-valent Pd complexes are potent agents for the oxidative functionalization of inert C-H bonds, and it was previously shown that rapid electrocatalytic methane monofunctionalization could be achieved by electro-oxidation of Pd II to a critical dinuclear Pd III intermediate in concentrated or fuming sulfuric acid. However, the structure of this highly reactive, unisolable intermediate, as well as the structural basis for its mechanism of electrochemical formation, remained elusive. Herein, we use X-ray absorption and Raman spectroscopies to assemble a structural model of the potent methane-activating intermediate as a Pd III dimer with a Pd-Pd bond and a 5-fold O atom coordination by H x SO 4 (x-2) ligands at each Pd center. We further use EPR spectroscopy to identify a mixed-valent M-M bonded Pd 2 II,III species as a key intermediate during the Pd II -to-Pd III 2 oxidation. Combining EPR and electrochemical data, we quantify the free energy of Pd dimerization as <-4.5 kcal/mol for Pd 2 II,III and <-9.1 kcal/mol for Pd III 2 . The structural and thermochemical data suggest that the aggregate effect of metal-metal and axial metal-ligand bond formation drives the critical Pd dimerization reaction in between electrochemical oxidation steps. This work establishes a structural basis for the facile electrochemical oxidation of Pd II to a M-M bonded Pd III dimer and provides a foundation for understanding its rapid methane functionalization reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

"Lignin First" Catalytic Biomass Fractionation: Cooperative Research and Development (Final Report)

In this work, a continuous zwitterionic chromatography using simulated moving beds will be conducted to separate Li and Mg from brines. The existing program that ExxonMobil is carrying out with Clariant and Genomatica is consistent with all pioneer cellulosic fuels plants inasmuch as biomass enters the facility and is processed, in its entirety, through at least the hydrolysis step of biochemical conversion. This approach creates significant operating challenges as biomass can vary widely in composition and mechanical properties across and within a given biomass type. The proposed program involves a first step fractionation using solvolysis and reductive catalysis to generate a lignin oil containing well-defined monomers, dimers, and oligomers and a delignified cellulose/ hemicellulose pulp. The amount of lignin oil vs pulp and the type of monomers produced are expected to vary with biomass type due to differences in lignin composition and chemistry.

09 BIOMASS FUELS↗
DOE OSTI2021

Mechanism of Metal Intercalation under Graphene through Small Vacancy Defects

Metal intercalation under graphene has attracted extensive experimental and theoretical research because of its capability to manipulate the electronic structure and properties of graphene. However, the pathways and mechanisms of intercalation are still not well understood. Here, we systematically investigate the intercalation process of metal atoms through graphene vacancies using first-principles calculations. We show that the energy barrier for metal atom penetration through the vacancies in graphene is small as long as the size of the vacancy is larger than a mono-vacancy. However, metal atoms are strongly bonded to the vacancy so that the detachment energy of a metal atom from the vacancy is extremely high. This inhibits the diffusion of the metal atom into the gallery beneath the surface to complete the intercalation process. On the other hand, our calculation results show that the detachment energy of a metal atom from a metal dimer at small vacancy defects is significantly reduced, making intercalation much easier. Therefore, the key step limiting the intercalation process is the detachment of the metal atoms from vacancy defects. This finding from our study provides useful insight into the defect-assisted intercalation mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

On the mechanism of soot nucleation

The mechanism of carbon particulate (soot) inception has been a subject of numerous studies and debates. The article begins with a critical review of prior proposals, proceeds to the analysis of factors enabling the development of a meaningful nucleation flux, and then introduces new ideas that lead to the fulfillment of these requirements. In the new proposal, a rotationally-activated dimer is formed in the collision of an aromatic molecule and an aromatic radical; the two react during the lifetime of the dimer to form a stable, doubly-bonded bridge between them, with the reaction rooted in a five-member ring present on the molecule edge. Several such reactions were examined theoretically and the most promising one generated a measurable nucleation flux. The consistency of the proposed model with known aspects of soot particle nanostructure is discussed. Here, the foundation of the new model is fundamentally the H-Abstraction-Carbon-Addition (HACA) mechanism with the reaction affinity enhanced by rotational excitation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

In Situ Identification of Reaction Intermediates and Mechanistic Understandings of Methane Oxidation over Hematite: A Combined Experimental and Theoretical Study

Effective methane utilization for either clean power generation or value-added chemical production has been a subject of growing attention worldwide for decades, yet challenges persist mostly in relation to methane activation under mild conditions. Here, we report hematite, an earth-abundant material, to be highly effective and thermally stable to catalyze methane combustion at low temperatures (<500 °C) with a low light-off temperature of 230 °C and 100% selectivity to CO 2 . The reported performance is impressive and comparable to those of precious-metal-based catalysts, with a low apparent activation energy of 17.60 kcal·mol –1 . Our theoretical analysis shows that the excellent performance stems from a tetra-iron center with an antiferromagnetically coupled iron dimer on the hematite (110) surface, analogous to that of the methanotroph enzyme methane monooxygenase that activates methane at ambient conditions in nature. Isotopic oxygen tracer experiments support a Mars van Krevelen redox mechanism where CH 4 is activated by reaction with a hematite surface oxygen first, followed by a catalytic cycle through a molecular-dioxygen-assisted pathway. Surface studies with in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) and density functional theory (DFT) calculations reveal the evolution of reaction intermediates from a methoxy CH 3 –O–Fe, to a bridging bidentate formate b-HCOO–Fe, to a monodentate formate m-HCOO–Fe, before CO 2 is eventually formed via a combination of thermal hydrogen-atom transfer (HAT) and proton-coupled electron transfer (PCET) processes. Finally, the elucidation of the reaction mechanism and the intermediate evolutionary profile may allow future development of catalytic syntheses of oxygenated products from CH 4 in gas-phase heterogeneous catalysis.

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

Structural basis for inhibition of the Cation-chloride cotransporter $\mathrm{NKCC1}$ by the diuretic drug bumetanide

Cation-chloride cotransporters (CCCs) NKCC1 and NKCC2 catalyze electroneutral symport of 1 Na + , 1K + , and 2 Cl - across cell membranes. NKCC1 mediates trans-epithelial Cl - secretion and regulates excitability of some neurons and NKCC2 is critical to renal salt reabsorption. Both transporters are inhibited by the so-called loop diuretics including bumetanide, and these drugs are a mainstay for treating edema and hypertension. Here, our single-particle electron cryo-microscopy structures supported by functional studies reveal an outward-facing conformation of NKCC1, showing bumetanide wedged into a pocket in the extracellular ion translocation pathway. Based on these and the previously published inward-facing structures, we define the translocation pathway and the conformational changes necessary for ion translocation. We also identify an NKCC1 dimer with separated transmembrane domains and extensive transmembrane and C-terminal domain interactions. We further define an N-terminal phosphoregulatory domain that interacts with the C-terminal domain, suggesting a mechanism whereby (de)phosphorylation regulates NKCC1 by tuning the strength of this domain association.

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

Vacancy-induced suppression of charge density wave order and its impact on magnetic order in kagome antiferromagnet FeGe

Two-dimensional (2D) kagome lattice metals are interesting because their corner sharing triangle structure enables a wide array of electronic and magnetic phenomena. Recently, post-growth annealing is shown to both suppress charge density wave (CDW) order and establish long-range CDW with the ability to cycle between states repeatedly in the kagome antiferromagnet FeGe. Here we perform transport, neutron scattering, scanning transmission electron microscopy (STEM), and muon spin rotation (μSR) experiments to unveil the microscopic mechanism of the annealing process and its impact on magneto-transport, CDW, and magnetism in FeGe. Annealing at 560 °C creates uniformly distributed Ge vacancies, preventing the formation of Ge-Ge dimers and thus CDW, while 320 °C annealing concentrates vacancies into stoichiometric FeGe regions with long-range CDW. The presence of CDW order greatly affects the anomalous Hall effect, incommensurate magnetic order, and spin-lattice coupling in FeGe, placing FeGe as the only kagome lattice material with tunable CDW and magnetic order.

critical phenomena↗
DOE OSTI2023

The Effect of Monomer Size on Fusion and Coupling in Colloidal Quantum Dot Molecules

The fusion step in the formation of colloidal quantum dot molecules, constructed from two core/shell quantum dots, dictates the coupling strength and hence their properties and enriched functionalities compared to monomers. Herein, studying the monomer size effect on fusion and coupling, we observe a linear relation of the fusion temperature with the inverse nanocrystal radius. This trend, similar to that in nanocrystal melting, emphasizes the role of the surface energy. The suggested fusion mechanism involves intraparticle ripening where atoms diffuse to the reactive connecting neck region. Moreover, the effect of monomer size and neck filling on the degree of electronic coupling is studied by combined atomistic-pseudopotential calculations and optical measurements, uncovering strong coupling effects in small QD dimers, leading to significant optical changes. Understanding and controlling the fusion and hence coupling effect allows tailoring the optical properties of these nanoscale structures, with potential applications in photonic and quantum technologies.

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

Metadynamics simulations reveal mechanisms of Na + and Ca 2+ transport in two open states of the channelrhodopsin chimera, C1C2

Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca 2+ permeability vs. Na + by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na + and Ca 2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca 2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.

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

Cristae formation is a mechanical buckling event controlled by the inner mitochondrial membrane lipidome

Cristae are high–curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae–shaping proteins have been defined, analogous lipid–based mechanisms have yet to be elucidated. Here, we combine experimental lipidome dissection with multi–scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the inner mitochondrial membrane against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein–mediated curvatures. This model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that cardiolipin is essential in low–oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of cardiolipin is dependent on the surrounding lipid and protein components of the IMM.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mechanisms of the Cu(I)-Catalyzed Intermolecular Photocycloaddition Reaction Revealed by Optical and X-ray Transient Absorption Spectroscopies

The [2 + 2] photocycloaddition provides a simple, single-step route to cyclobutane moieties that would otherwise be disfavored or impossible due to ring strain and/or steric interactions. We have used a combination of optical and X-ray transient absorption spectroscopies to elucidate the mechanism of the Cu(I)-catalyzed intermolecular photocycloaddition reaction using norbornene and cyclohexene as model substrates. We find that for norbornene the reaction proceeds through an initial metal-to-ligand charge transfer (MLCT) state that persists for 18 ns before the metal returns to the monovalent oxidation state. The Cu K-edge spectrum continues to evolve until ~5 μs and then remains unchanged for the 50 μs duration of the measurement, reflecting product formation and ligand dissociation. We hypothesize that the MLCT transition and reverse electron transfer serve to sensitize the triplet excited state of one of the norbornene ligands, which then dimerizes with the other to give the product. For the case of cyclohexene, however, we do not observe a charge transfer state following photoexcitation and instead find evidence for an increase in the metal–ligand bond strength that persists for several ns before product formation occurs. This is consistent with a mechanism in which ligand photoisomerization is the initial step, which was first proposed by Salomon and Kochi in 1974 to explain the stereoselectivity of the reaction. Furthermore, our investigation reveals how this photocatalytic reaction may be directed along strikingly disparate trajectories by only very minor changes to the structure of the substrate.

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

Distinct Mechanisms of Triplet Pair Decay in Amorphous and Crystalline Heteroacene Thin Films

Triplet pairs (TT) in crystalline molecular semiconductors have unique spin properties of interest for quantum information or enhancing solar photoconversion. The population and diffusion dynamics of TT have been the subject of recent studies, both in covalent dimers and in crystalline systems. Here, in this study, we monitor the triplet population in neat polycrystalline and amorphous films of a heteroacene with known TT spectral properties and tunable spin polarization depending on the intermolecular geometry. Transient measurements reveal an anomalous power dependence in polycrystalline films that we attribute to the fast diffusion and interaction of dissociated triplet pairs confined to one-dimensional stacks of strongly coupled molecules. The nongeminate triplet interaction after dephasing facilitates conversion to the triplet 3 TT and eventually T 1 +S 0 . Amorphous films have no power dependence and proceed directly from 1 TT to 3 TT and subsequently T 1 +S 0 via state mixing facilitated by nonparallel geometries and weak exchange coupling.

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

ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA, which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question, we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes, including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a WYL motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD structures reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated operator DNA binding activation. Biochemical and in vivo studies support the structural model. Our data thus reveal the molecular mechanism underpinning an SOS-independent DNA damage repair pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural insights into RNA cleavage by a novel family of bacterial RNases

Abstract Processing of RNA is a key regulatory mechanism for all living systems. Escherichia coli protein YicC belongs to the well-conserved YicC family and has been identified as a novel ribonuclease. Here, we report a 2.8-Å-resolution crystal structure of the E. coli YicC apo protein and a 3.2-Å-cryo-EM structure of YicC bound to an RNA substrate. The apo YicC forms a dimer of trimers with a large open channel. In the RNA-bound form, the top trimer of YicC rotates nearly 70° and closes the RNA substrate inside the cavity to form a clamshell-pearl conformation that resembles no other known RNases. The structural information combined with mass spectrometry and biochemical data identified cleavage on the upstream side of an RNA hairpin. Mutagenesis studies demonstrated that the previously uncharacterized domain, DUF1732, is critical in both RNA binding and catalysis. These studies shed light on the mechanism of the previously unexplored YicC RNase family.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Unraveling Triplet Formation Mechanisms in Acenothiophene Chromophores

The evolution of molecular platforms for singlet fission (SF) chromophores has fueled the quest for new compounds capable of generating triplets quantitatively at fast time scales. As the exploration of molecular motifs for SF has diversified, a key challenge has emerged in identifying when the criteria for SF have been satisfied. Here, we show how covalently bound molecular dimers uniquely provide a set of characteristic optical markers that can be used to distinguish triplet pair formation from processes that generate an individual triplet. These markers are contained within (i) triplet charge-transfer excited state absorption features, (ii) kinetic signatures of triplet-triplet annihilation processes, and (iii) the modulation of triplet formation rates using bridging moieties between chromophores. Our assignments are verified by time-resolved electron paramagnetic resonance (EPR) measurements, which directly identify triplet pairs by their electron spin and polarization patterns. Here we apply these diagnostic criteria to dimers of acenothiophene derivatives in solution that were recently reported to undergo efficient intermolecular SF in condensed media. While the electronic structure of these heteroatom-containing chromophores can be broadly tuned, the effect of their enhanced spin-orbit coupling and low-energy nonbonding orbitals on their SF dynamics has not been fully determined. We find that SF is fast and efficient in tetracenothiophene but that anthradithiophene exhibits fast intersystem crossing due to modifications of the singlet and triplet excited state energies upon functionalization of the heterocycle. We conclude that it is not sufficient to assign SF based on comparisons of the triplet formation kinetics between monomer and multichromophore systems.

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

Spin-Vibronic Effect in Photoinduced Electron Transfer

The spin-vibronic effect (SVE) accelerates quantum-mechanically forbidden electronic transitions, but experimental manifestations of this phenomenon remain limited. In this contribution, the role of SVE in photoinduced electron transfer (PET) dynamics is probed by coherent vibrational wavepacket (CVWP) motions in Pt­(II) dimer-naphthalene diimide donor–acceptor complexes. Metal–metal-to-ligand charge-transfer (MMLCT) excitation of the donor triggers ballistic PET, driving the molecule away from equilibrium. The SVE then directs the PET trajectory from the 1 MMLCT excited state to an intermediate ligand-centered triplet state, modulating the CVWP dynamics along the reaction coordinates. Herzberg–Teller type oscillations indicate that the Pt–Pt stretching vibration, arising from the formation of the excited triplet intermediate, serves as the reaction coordinate for charge separation. Finally, our experimental findings advance the understanding of the interplay between electronic, vibrational, and spin degrees of freedom in ultrafast photoactivated processes.

Kim, Pyosang [Argonne National Laboratory (ANL), A↗