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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.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Mechanisms of Al3+ dimerization in alkaline solutions

The molecular speciation of aluminum (Al3+) in alkaline solutions is fundamental to its precipitation chemistry within a number of industrial applications that include ore renement and industrial processing of Al wastes. Under these conditions, Al3+ is predominantly Al(OH) {4 , while at high [Al] dimeric species also known to form. To date, the mechanism of dimer formation remains unclear and it is likely infuenced by complex ion ion interactions. In the present work, we investigate the role of ion pairing and a suite of potential dimerization pathways using a three-pronged approach that consists of density functional theory-based molecular dynamics (DFTMD), static DFT calculations (sDFT) and semi-empirical density functional tight binding molecular dynamics (SEMD). Specic cation eects imparted by the background electrolyte cations Na+, Li+ and K+ have been examined. Our simulations predict that when the Al species are ion paired with either cation the formation of the oxo-bridged Al2O(OH) 2{6 is favored with respect to the dihydroxo-bridged Al2(OH) 2{8 , in agreement with previousspectroscopic work. The formation of both dimers rst proceeds by bridging of two monomeric units via one hydroxo ligand, leading to a labile Al2(OH) 2{8 isomer. The eect of contact ion pairing of Li+ and K+ on the dimerization energetics is distinctly more favorable than that of Na+, which may have an impact on further ligomerization.

Pouvreau, Maxime↗
DOE OSTI2023

A Nonorthogonal Configuration Interaction Approach to Singlet Fission in Perylenediimide Compounds

Perylenediimide molecules constitute a family of chromophores that undergo singlet fission, a process in which an excited singlet state converts into lower energy triplets on two neighboring molecules, potentially increasing the efficiency of organic solar cells. Here, the nonorthogonal configuration interaction method is applied to study the effect of the different crystal packing of various perylenediimide derivatives on the relative energies of the singlet and triplet states, the intermolecular electronic couplings, and the relative rates for singlet fission. The analysis of the wave functions and electronic couplings reveals that charge transfer states play an important role in the singlet fission mechanism. Dimer conformations where the PDI molecules are at large displacements along the long axis and short on the short axis are posed as the most favorable for singlet fission. The role of the substituent at the imide group has been inspected concluding that, although it has no effect in the energies, for some conformations it significantly influences the electronic couplings, and therefore, replacing this substituent with hydrogen may introduce artifacts in the computational modeling of the PDI molecules.

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

Entangled Electrons Drive a Non-superexchange Mechanism in a Cobalt Quinoid Dimer Complex

A central theme in chemistry is the understanding of the mechanisms that drive chemical transformations. A well-known, highly cited mechanism in organometallic chemistry is the superexchange mechanism in which unpaired electrons on two or more metal centers interact through an electron pair of the bridging ligand. We use a combination of novel synthesis and computation to show that such interactions may in fact occur by a more direct mechanism than superexchange that is based on direct quantum entanglement of the two metal centers. Specifically, we synthesize and experimentally characterize a novel cobalt dimer complex with benzoquinoid bridging ligands and investigate its electronic structure with the variational two-electron reduced density matrix method using large active spaces. The result draws novel connections between inorganic mechanisms and quantum entanglement, thereby opening new possibilities for the design of strongly correlated organometallic compounds whose magnetic and spin properties have applications in superconductors, energy storage, thermoelectrics, and spintronics.

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

Structural basis for SHOC2 modulation of RAS signalling

The RAS–RAF pathway is one of the most commonly dysregulated in human cancers. Despite decades of study, understanding of the molecular mechanisms underlying dimerization and activation of the kinase RAF remains limited. Recent structures of inactive RAF monomer and active RAF dimer bound to 14-3-3 have revealed the mechanisms by which 14-3-3 stabilizes both RAF conformations via specific phosphoserine residues. Prior to RAF dimerization, the protein phosphatase 1 catalytic subunit (PP1C) must dephosphorylate the N-terminal phosphoserine (NTpS) of RAF to relieve inhibition by 14-3-3, although PP1C in isolation lacks intrinsic substrate selectivity. SHOC2 is as an essential scaffolding protein that engages both PP1C and RAS to dephosphorylate RAF NTpS, but the structure of SHOC2 and the architecture of the presumptive SHOC2–PP1C–RAS complex remain unknown. Here we present a cryo-electron microscopy structure of the SHOC2–PP1C–MRAS complex to an overall resolution of 3Å, revealing a tripartite molecular architecture in which a crescent-shaped SHOC2 acts as a cradle and brings together PP1C and MRAS. Our work demonstrates the GTP dependence of multiple RAS isoforms for complex formation, delineates the RAS-isoform preference for complex assembly, and uncovers how the SHOC2 scaffold and RAS collectively drive specificity of PP1C for RAF NTpS. Our data indicate that disease-relevant mutations affect complex assembly, reveal the simultaneous requirement of two RAS molecules for RAF activation, and establish rational avenues for discovery of new classes of inhibitors to target this pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. Furthermore, the relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein–Frenkel Hamiltonian model.

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

Dimer Asymmetry and Light Activation Mechanism in Brucella Blue-Light Sensor Histidine Kinase

The ability to sense and respond to environmental cues is essential for adaptation and survival in living organisms. In bacteria, this process is accomplished by multidomain sensor histidine kinases that undergo autophosphorylation in response to specific stimuli, thereby triggering downstream signaling cascades. However, the molecular mechanism of allosteric activation is not fully understood in these important sensor proteins. Here, we report the full-length crystal structure of a blue light photoreceptor LOV histidine kinase (LOV-HK) involved in light-dependent virulence modulation in the pathogenic bacterium Brucella abortus. Joint analyses of dark and light structures determined in different signaling states have shown that LOV-HK transitions from a symmetric dark structure to a highly asymmetric light state. The initial local and subtle structural signal originated in the chromophore-binding LOV domain alters the dimer asymmetry via a coiled-coil rotary switch and helical bending in the helical spine. These amplified structural changes result in enhanced conformational flexibility and large-scale rearrangements that facilitate the phosphoryl transfer reaction in the HK domain.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A split luciferase system for studying coronavirus Mpro dimerization in vitro and in living cells

The main protease enzyme (Mpro) of coronaviruses cleaves the viral polyprotein into functional units essential for virus replication. Prior work has demonstrated that Mpro functions as a homodimer. However, studies on the mechanism of dimerization have been challenging because the purified protease is mostly dimeric, dimerization-defective mutants lack proteolytic activity, and robust cell-based assays have yet to be reported. To enable work on Mpro dimerization, we have developed a quantitative luciferase-based SARS-CoV-2 (SARS2) Mpro biosensor that accurately reports protein dimerization in living cells and, upon purification, also in vitro. Co-transfection of cells with a construct expressing Mpro fused to the 18 kDa LargeBiT of luciferase (LgBiT) and a second construct with Mpro fused to the 1 kDa SmallBiT of luciferase (SmBiT) results in a reconstitution of luciferase activity in a dose-dependent manner that requires conserved residues within the dimerization interface. Proteolytic activity is dispensable for dimerization and, uniquely, a C145A catalytically inactive mutant exhibits enhanced dimerization signal likely due to lower cytotoxicity. Mpro enzymes from multiple different coronaviruses also dimerize in this system, indicating mechanistic conservation. Interestingly, this dimerization biosensor also provides a quantitative read-out of inhibitor-facilitated dimerization. Covalent SARS2 Mpro inhibitors such as nirmatrelvir cause a 3- to 5-fold increase in luciferase activity. Together with corroborating structural, biophysical, and molecular dynamics experiments, our studies support a model in which covalent Mpro inhibitors such as nirmatrelvir simultaneously block catalytic activity and induce allosteric stabilization of the dimeric complex.

SARS-CoV-2 main protease (Mpro/3CLpro)↗
DOE OSTI2023

Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions

A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.

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

Structure of coxsackievirus cloverleaf RNA and 3C pro dimer establishes the RNA-binding mechanism of enterovirus protease 3C pro

In positive-strand RNA viruses, the genome serves as a template for both protein translation and negative-strand RNA synthesis. Enteroviruses use the cloverleaf RNA structure at the 5′ end of the genome to balance these two processes. Cloverleaf acts as a promoter for RNA synthesis and forms a complex with viral 3CD protein, the precursor to 3C pro protease, and 3D pol polymerase. The interaction between cloverleaf and 3CD is mediated by the 3C pro domain, yet how 3C pro promotes specific RNA-binding is not clear. We report the structure of coxsackievirus cloverleaf RNA-3C pro complex, wherein two 3C pro molecules interact with cloverleaf stem-loop D. 3C pro dimer mainly recognizes the shape of the dsRNA helix through symmetric interactions, suggesting that 3C pro is a previously undiscovered type of RNA binding protein. We show that 3CD protein also dimerizes on cloverleaf RNA and binds the RNA with higher affinity than 3C pro . The structure provides insight into the RNA-binding mechanism of 3C pro or 3CD with other cis-acting replication elements.

Science & Technology - Other Topics↗
DOE OSTI2024

The CNK–HYP scaffolding complex promotes RAF activation by enhancing KSR–MEK interaction

The RAS–MAPK pathway regulates cell proliferation, differentiation and survival, and its dysregulation is associated with cancer development. The pathway minimally comprises the small GTPase RAS and the kinases RAF, MEK and ERK. Activation of RAF by RAS is notoriously intricate and remains only partially understood. There are three RAF isoforms in mammals (ARAF, BRAF and CRAF) and two related pseudokinases (KSR1 and KSR2). RAS-mediated activation of RAF depends on an allosteric mechanism driven by the dimerization of its kinase domain. Recent work on human RAFs showed that MEK binding to KSR1 promotes KSR1–BRAF heterodimerization, which leads to the phosphorylation of free MEK molecules by BRAF. Similar findings were made with the single Drosophila RAF homolog. Here we show that the fly scaffold proteins CNK and HYP stabilize the KSR–MEK interaction, which in turn enhances RAF–KSR heterodimerization and RAF activation. The cryogenic electron microscopy structure of the minimal KSR–MEK–CNK–HYP complex reveals a ring-like arrangement of the CNK–HYP complex allowing CNK to simultaneously engage KSR and MEK, thus stabilizing the binary interaction. Together, these results illuminate how CNK contributes to RAF activation by stimulating the allosteric function of KSR and highlight the diversity of mechanisms impacting RAF dimerization as well as the regulatory potential of the KSR–MEK interaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Catalytic Site Requirements for N2O Decomposition on Cu-, Co-, and Fe-SSZ-13 Zeolites

N2O decomposition is investigated on Cu, Co and Fe-exchanged SSZ-13 zeolite catalysts at relatively low metal loadings. The catalysts are synthesized by solution ion exchange, and subjected to X-ray diffraction (XRD), temperature-programed-reduction by H2 (H2-TPR), temperature-programed-reaction of N2O (N2O-TPR) coupled with in-situ transmission FTIR, and finally steady-state flow reaction tests. At low N2O pressures (< 0.05 kPa), all catalysts display pseudo first-order kinetics. From Arrhenius analysis, Cu and Fe-SSZ-13 display very different apparent activation energies but similar pre-exponential factors, suggesting their similar reaction mechanisms. N2O decomposition follows a dual-site mechanism, occurring on dimeric M-O-M sites in these catalysts, and O2 is formed by the combination of two O ad-atoms from two vicinal metal sites. Under low N2O pressure (0.05 kPa) and first-order kinetic regime, the reaction is limited by N-O cleavage on bare metal active sites. In comparison to Cu-SSZ-13, the much higher N2O decomposition rate over Fe-SSZ-13 is attributed to the much lower activation barriers for the N-O cleavage step. N2O decomposition occurs on isolated Co2+ ions in Co-SSZ-13. The rate-limiting step is N-O cleavage on an O-occupied Co site in the low-pressure first order kinetic regime. This single-site mechanism leads to much higher pre-exponential factors as compared to the dual-site mechanism. This beneficial factor for reaction rate enhancement, however, is compromised by the much higher activation barriers over this catalyst.

Lin, Fan↗
DOE OSTI2020

Effect of hydride vapor phase epitaxy growth conditions on the degree of atomic ordering in GaInP

We report a systematic study of CuPt-type ordering in hydride vapor phase epitaxy (HVPE)-grown Ga 0.5 In 0.5 P. Selected-area electron diffraction reveals ordering in samples grown on (001) GaAs substrates offcut toward (1$\overline{1}$1)B. The ordering is single-variant, occurring only on (1$\overline{1}$1)B planes and not on ($\overline{1}$11)B. Quantitative analysis of the order parameter by high-resolution x-ray diffraction (HRXRD) indicates that ordering increases with deposition temperature in samples grown at 600–700 °C with a constant gas-phase V/III ratio ~3. Ordering increases with V/III ratio in the range of 1.3–6.7 at a constant deposition temperature of 650°C. Photoluminescence measurements correlate the order parameter with Ga0.5In0.5P bandgap contraction, though the contraction is larger than expected based on the magnitude of order parameters measured by HRXRD. A possible reason for this discrepancy is that the photoluminescence emission occurs in the lower bandgap ordered domains, which are small and evenly dispersed throughout the material. We also show that the degree of ordering decreases with growth rate, disappearing at ~60 µm/h. The HVPE-grown material exhibits a generally weaker ordering than organometallic vapor phase epitaxy (OMVPE)-grown material, likely due to the moderate V/III ratios employed, in contrast to the V/III ratios in the 100s typical of OMVPE. However, the tendency for ordering to increase with V/III ratio suggests that the same dimer-induced stress mechanism used to explain the occurrence of ordering in OMVPE-grown material also applies to HVPE. The tendencies for ordering to increase with deposition temperature and decrease with growth rate show that kinetics limit the degree of ordering, also in agreement with OMVPE trends.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

Assembly and Repair of Photosystem II in Chlamydomonas reinhardtii

Oxygenic photosynthetic organisms use Photosystem II (PSII) to oxidize water and reduce plastoquinone. Here, we review the mechanisms by which PSII is assembled and turned over in the model green alga Chlamydomonas reinhardtii. This species has been used to make key discoveries in PSII research due to its metabolic flexibility and amenability to genetic approaches. PSII subunits originate from both nuclear and chloroplastic gene products in Chlamydomonas. Nuclear-encoded PSII subunits are transported into the chloroplast and chloroplast-encoded PSII subunits are translated by a coordinated mechanism. Active PSII dimers are built from discrete reaction center complexes in a process facilitated by assembly factors. The phosphorylation of core subunits affects supercomplex formation and localization within the thylakoid network. Proteolysis primarily targets the D1 subunit, which when replaced, allows PSII to be reactivated and completes a repair cycle. While PSII has been extensively studied using Chlamydomonas as a model species, important questions remain about its assembly and repair which are presented here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Experimental and quantum mechanical characterization of an oxygen-bridged plutonium(IV) dimer

We report the synthesis and characterization of K 4 {[PuCl 2 (NO 3 ) 3 ] 2 (μ 2 -O)}·H 2 O, which contains the first known μ 2 -oxo bridge between two Pu IV metal centers. Adding to its uniqueness is the Pu-(μ 2 -O) bond length of 2.04 Å, which is the shortest of other analogous compounds. The Pu-(μ 2 -O)-Pu bridge is characterized by the mixing of s -, d -, and p -orbitals from Pu with the p -orbitals of O; the 5 f -orbitals do not participate in bonding. Natural bond orbital analysis indicates that Pu and O interact through one 3c-2e σ Pu-O-Pu and two 3c-2e π Pu-O-Pu bonding orbitals and that the electron density is highly polarized on the μ 2 -O. Bond topology properties analysis indicates that the Pu-(μ 2 -O) bond shares both ionic and covalent character. Quantum mechanical calculations also show that the dimer has multiconfigurational ground states, where the nonet, septet, quintet, triplet, and singlet are close in energy. This work demonstrates the interplay between experimental and computational efforts that is required to understand the chemical bonding of Pu compounds.

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

On the mechanism of soot nucleation. II. E-bridge formation at the PAH bay

A recently proposed mechanism of soot nucleation based upon the formation of a rotationally-activated dimer in the collision of an aromatic molecule and a radical leading to a stable, doubly-bonded E-bridge between them, rooted in the existence of a five-membered ring on the molecule edge, has been further investigated with a focus on the 5-6 E-bridge forming in the reaction of a PAH cyclopenta group with a bay site of another PAH. As a prototype reaction of this kind, we examined the reaction between 4-phenanthrenyl and acenaphthylene and, to project these results to larger aromatic structures, we also explored the size effect of the E-bridge forming reactions by computing the 1-naphthyl + acenaphthylene system and comparing these results with the prior results for pyrenyl + acepyrene. The two systems have been studied through high-level G3(MP2,CC)//B3LYP/6-311G(d,p) ab initio calculations of their potential energy surfaces combined with the RRKM/Master Equation calculations of reaction rate constants. With PAH monomers of similar sizes involved, the formation of E-bridge structures at the bay radical sites appeared to be faster and lead to increased nucleation rates as compared to the zigzag-forming ones. Furthermore, a model combining both the bay and zigzag rotationally-induced formation of E-bridges successfully reaches the level of nucleation fluxes comparable to those of the irreversible pyrene dimerization, thus affirming the rotationally-activated dimerization as a feasible mechanism for soot particle nucleation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗