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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Solid-state dimer method for calculating solid-solid phase transitions

The dimer method is a minimum mode following algorithm for finding saddle points on a potential energy surface of atomic systems. Here, the dimer method is extended to include the cell degrees of freedom for periodic solid-state systems. Using this method, reaction pathways of solid-solid phase transitions can be determined without having to specify the final state structure or reaction mechanism. Example calculations include concerted phase transitions between CdSe polymorphs and a nucleation and growth mechanism for the A15 to BCC transition in Mo.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

On the validity of the basis set superposition error and complete basis set limit extrapolations for the binding energy of the formic acid dimer

We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for D{sub e} = − 16.1 ± 0.1 kcal/mol and for D{sub 0} = − 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of −14.22 ± 0.12 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Insights into PG-binding, conformational change, and dimerization of the OmpA C-terminal domains from Salmonella enterica serovar Typhimurium and Borrelia burgdorferi : Characterization of OmpA C-Terminal Domain

S. Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins of the bacterium. OmpA is one of these major OM proteins. It comprises a N-terminal eight-stranded -barrel membrane domain and a C-terminal so-called OmpA C-terminal domain (OmpACTD). The OmpACTD and its homologs are believed to bind to peptidoglycan (PG) within the periplasm, maintaining bacterial osmotic homeostasis and modulating the permeability and integrity of the outer membrane. Here we present the structures of two forms of the OmpACTD of S. Typhimurium (STOmpACTD) and one structure of the less-studied OmpACTD of Borrelia burgdorferi (BbOmpACTD). In the open form of STOmpACTD, an aspartic acid residue from a long 2-3 loop points into the binding pocket, suggesting that an anion group such as a carboxylate group from PG is favored at the binding site. In the closed form of STOmpACTD and in the structure of BbOmpACTD, a sulfate group from the crystallization buffer is tightly bound at the equivalent site. The differences between the closed and open forms of STOmpACTD, suggest a large conformational change that includes an extension of 3 helix by ordering a part of 2-3 loop. We suggest that the sulfate anion observed in these structures mimics the carboxylate group of PG when bound to STOmpACTD. In addition, the binding of PG or a ligand mimic may enhance dimerization of STOmpACTD, or possibly that of full length STOmpA.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2023

Highly Coupled Heterobicycle‐Fused Porphyrin Dimers: Excitonic Coupling and Charge Separation with Coordinated Fullerene, C 60

Abstract Porphyrin dimers have been widely explored and studied owing to their importance in photosynthetic systems. A vast variety of dimers linked by different groups and at different angles have been synthesized and studied; however, the means by which to synthesize rigidly fused porphyrins with direct conjugation of the chromophores remains limited. Such a class of porphyrins may possess interesting properties that unconjugated or stacked dimers may not exhibit. In this study, bisbenzimidazole‐fused porphyrin dimers and their mono‐ and bis−zinc derivatives are synthesized and characterized. As a consequence of excitonic coupling, these dimers exhibit a split Soret band irrespective of the metal ion in the porphyrin cavity. Steady‐state fluorescence and excitation spectra followed by femtosecond transient absorption spectral studies of the heterometallated dimer, (free‐base and zinc porphyrin) reveals the occurrence of efficient singlet‐singlet energy transfer (>95 % efficiency and rate constant >10 12 s −1 ) within the dyad. Further, donor‐acceptor conjugates were formed by metal‐ligand axial coordination of phenyl imidazole functionalized C 60 and were characterized by a variety of physicochemical techniques. Excited state charge separation from both singlet and triplet excited states of ZnP in the conjugates has been established. The lifetime of the final charge‐separated state was in the 30–40 μs range revealing charge stabilization. Interestingly, no charge separation in the conjugate derived from the heterometallated dimer was observed wherein excitation transfer dominated the process. The present study brings out the importance of the rigid π‐spacer connecting porphyrin dimers in governing the energy and electron transfer events when coupled with an electron acceptor.

Chemistry↗
DOE OSTI2014

Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair

Highlights: • ATM phosphorylates the opposite strand of the dimer in response to DNA damage. • The PETPVFRLT box of ATM plays a key role in its dimer dissociation in DNA repair. • The dephosphorylation of ATM is critical for dimer re-formation after DNA repair. - Abstract: The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Tracing intermolecular Coulombic decay of carbon-dioxide dimers and oxygen dimers after valence photoionization

In this study, we have conducted an experimental study on the photo double ionization (PDI) of carbon-dioxide dimers at photon energies of 37 and 55 eV and oxygen dimers at photon energies of 38, 41.5, and 46 eV, while focusing on the dissociation dynamics upon single-photon absorption. The investigation was performed by applying the cold-target recoil-ion momentum spectroscopy method in order to collect and record the three-dimensional momenta of the ionic fragments and emitted electrons from the dissociating dimer in coincidence. The kinetic-energy release upon fragmentation and the electron angular distributions in the laboratory and body-fixed frames, as well as the relative electron-electron emission angle, show unambiguous experimental evidence of intermolecular Coulombic decay (ICD) in carbon-dioxide dimers upon photoionization below and above the double-ionization threshold of CO 2 monomers. The PDI of oxygen dimers is less conclusive and shows contributions from ICD and knock-off ionization mechanisms. As for atomic dimers, the present results reveal that ICD in CO 2 dimers after valence PDI can also serve as a source for low-energy electrons, known to be very relevant in biological systems, cells, and tissues.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2017

Dipole Approximation to Predict the Resonances of Dimers Composed of Dielectric Resonators for Directional Emission: Dielectric Dimers Dipole Approximation

In this paper we develop a fully-retarded, dipole approximation model to estimate the effective polarizabilities of a dimer made of dielectric resonators. They are computed from the polarizabilities of the two resonators composing the dimer. We analyze the situation of full-cubes as well as split-cubes, which have been shown to exhibit overlapping electric and magnetic resonances. We compare the effective dimer polarizabilities to ones retrieved via full-wave simulations as well as ones computed via a quasi-static, dipole approximation. We observe good agreement between the fully-retarded solution and the full-wave results, whereas the quasi-static approximation is less accurate for the problem at hand. The developed model can be used to predict the electric and magnetic resonances of a dimer under parallel or orthogonal (to the dimer axis) excitation. This is particularly helpful when interested in locating frequencies at which the dimer will emit directional radiation.

42 ENGINEERING↗
DOE OSTI2014

Emergence of long-range order in sheets of magnetic dimers

Quantum spins placed on the corners of a square lattice can dimerize and form singlets, which then can be transformed into a magnetic state as the interactions between dimers increase beyond threshold. This is a strictly 2D transition in theory, but real-world materials often need the third dimension to stabilize long-range order. We use high pressures to convert sheets of Cu2+ spin 1/2 dimers from local singlets to global antiferromagnet in the model system SrCu2(BO3)2. Single-crystal neutron diffraction measurements at pressures above 5 GPa provide a direct signature of the antiferromagnetic ordered state, whereas high-resolution neutron powder and X-ray diffraction at commensurate pressures reveal a tilting of the Cu spins out of the plane with a critical exponent characteristic of 3D transitions. The addition of anisotropic, interplane, spin–orbit terms in the venerable Shastry–Sutherland Hamiltonian accounts for the influence of the third dimension.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Ankyrin repeats as a dimerization module

Highlights: • We determined crystal structure of Legionella effector AnkC. • The structure displays seven ankyrin repeats with unique structural features. • AnkC dimerizes using outer surface of loops between ankyrin repeats. • This is the first example of ankyrin repeats-mediated dimerization. Legionella pneumophila is a pathogen, causing severe pneumonia in humans called Legionnaires' disease. AnkC (LegA12) is a poorly characterized 495-residue effector protein conserved in multiple Legionella species. Here, we report the crystal structure of a C-terminally truncated AnkC (2–384) at 3.2 Å resolution. The structure shows seven ankyrin repeats (ARs) with unique structural features. AnkC forms a dimer along the outer surface of loops between ARs. The dimer exists both in the crystal form and in solution, as shown by analytical ultracentrifugation. This is the first example of ARs as a dimerization module as opposed to solely a protein interaction domain. In addition, a novel α-helix insert between AR3-AR4 is positioned across the surface opposite the ankyrin groove. Sequence conservation suggests that the ankyrin groove of AnkC is a functional site that interacts with binding targets. This ankyrin domain structure is an important step towards a functional characterization of AnkC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

An MS-CASPT2 Calculation of the Excited Electronic States of an Axial Difluoroborondipyrromethene (BODIPY) Dimer

The previously reported (Duman et al., J. Org. Chem. 2012, 77, 4516) calculated state energies of monomeric difluoroborondipyrromethene (BODIPY) and its axial dimer would suggest that these dyes are promising candidates for singlet fission, and the dimer was computed to have an unusual low-lying doubly excited state. We find that these results were affected by the use of an imbalanced active space in multireference calculations and are not correct. Multistate complete-active-space second-order perturbation theory (MS-CASPT2/cc-pVDZ) calculations using an [8,8] (8 electrons in 8 orbitals) active space for the monomer and a [16,16] active space for the dimer reproduce quite well the observed excitation energies of the S 1 states of both, and yield T 1 excitation energies well in excess of half of the S 1 excitation energies. We conclude that neither BODIPY monomer nor its axial dimer would permit exothermic singlet fission and are not worthy of investigation as potentially useful candidates, and that the unusual low-energy doubly excited states of the dimer were artifacts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗