Search NASA⌕ Search

SEARCH · Search NASA

Results for “DIMERS”

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 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 OSTI2012

Structure and dimerization of translation initiation factor aIF5B in solution

Translation initiation factor 5B (IF5B) is required for initiation of protein synthesis. The solution structure of archaeal IF5B (aIF5B) was analysed by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) and was indicated to be in both monomeric and dimeric form. Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) of aIF5B indicated that aIF5B forms irreversible dimers in solution but only to a maximum of 5.0-6.8% dimer. Sedimentation velocity (SV) AUC at higher speed also indicated the presence of two species, and the sedimentation coefficients s{sub 20,w}{sup 0} were determined to be 3.64 and 5.51 {+-} 0.29 S for monomer and dimer, respectively. The atomic resolution (crystallographic) structure of aIF5B (Roll-Mecak et al. [6]) was used to model monomer and dimer, and theoretical sedimentation coefficients for these models were computed (3.89 and 5.63 S, respectively) in good agreement with the sedimentation coefficients obtained from SV analysis. Thus, the structure of aIF5B in solution must be very similar to the atomic resolution structure of aIF5B. SAXS data were acquired in the same buffer with the addition of 2% glycerol to inhibit dimerization, and the resultant monomeric aIF5B in solution did indeed adopt a structure very similar to the one reported earlier for the protein in crystalline form. The p(r) function indicated an elongated conformation supported by a radius of gyration of 37.5 {+-} 0.2 {angstrom} and a maximum dimension of {approx}130 {angstrom}. The effects of glycerol on the formation of dimers are discussed. This new model of aIF5B in solution shows that there are universal structural differences between aIF5B and the homologous protein IF2 from Escherichia coli.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2012

Structural and Biochemical Studies on the Regulation of Biotin Carboxylase by Substrate Inhibition and Dimerization

Biotin carboxylase (BC) activity is shared among biotin-dependent carboxylases and catalyzes the Mg-ATP-dependent carboxylation of biotin using bicarbonate as the CO{sub 2} donor. BC has been studied extensively over the years by structural, kinetic, and mutagenesis analyses. Here we report three new crystal structures of Escherichia coli BC at up to 1.9 {angstrom} resolution, complexed with different ligands. Two structures are wild-type BC in complex with two ADP molecules and two Ca{sup 2+} ions or two ADP molecules and one Mg{sup 2+} ion. One ADP molecule is in the position normally taken by the ATP substrate, whereas the other ADP molecule occupies the binding sites of bicarbonate and biotin. One Ca{sup 2+} ion and the Mg{sup 2+} ion are associated with the ADP molecule in the active site, and the other Ca{sup 2+} ion is coordinated by Glu-87, Glu-288, and Asn-290. Our kinetic studies confirm that ATP shows substrate inhibition and that this inhibition is competitive against bicarbonate. The third structure is on the R16E mutant in complex with bicarbonate and Mg-ADP. Arg-16 is located near the dimer interface. The R16E mutant has only a 2-fold loss in catalytic activity compared with the wild-type enzyme. Analytical ultracentrifugation experiments showed that the mutation significantly destabilized the dimer, although the presence of substrates can induce dimer formation. The binding modes of bicarbonate and Mg-ADP are essentially the same as those to the wild-type enzyme. However, the mutation greatly disrupted the dimer interface and caused a large re-organization of the dimer. The structures of these new complexes have implications for the catalysis by BC.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2012

Electron transfer beyond the static picture: A TDDFT/TD-ZINDO study of a pentacene dimer

We use time-dependent density functional theory and time-dependent ZINDO (a semi-empirical method) to study transfer of an extra electron between a pair of pentacene molecules. A measure of the electronic transfer integral is computed in a dynamic picture via the vertical excitation energy from a delocalized anionic ground state. With increasing dimer separation, this dynamical measurement of charge transfer is shown to be significantly larger than the commonly used static approximation (i.e., LUMO+1–LUMO of the neutral dimer, or HOMO–LUMO of the charged dimer), up to an order of magnitude higher at 6 Å. These results offer a word of caution for calculations involving large separations, as in organic photovoltaics, where care must be taken when using a static picture to model charge transfer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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 OSTI2014

Band gap of epitaxial in-plane-dimerized single-phase NbO{sub 2} films

We demonstrate the epitaxial growth of high quality crystalline phase-pure NbO{sub 2} films on various oxide substrates using molecular beam epitaxy. Using a combination of reflection high-energy electron diffraction and x-ray diffraction we show that the films grow with the pseudo-rutile (100) orientation out of plane. The band gap of the NbO{sub 2} films is determined to be at least 1.0 eV using a combination of x-ray photoelectron spectroscopy and inverse photoelectron spectroscopy, in conjunction with hybrid density functional calculations of the density of states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗