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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
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↗
DOE OSTI2015

Dimeric c-di-GMP is required for post-translational regulation of alginate production in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen that secretes the exopolysaccharide alginate during infection of the respiratory tract of individuals afflicted with cystic fibrosis and chronic obstructive pulmonary disease. Among the proteins required for alginate production, Alg44 has been identified as an inner membrane protein whose bis-(3',5')-cyclic dimeric guanosine monophosphate (c-di-GMP) binding activity post-translationally regulates alginate secretion. In this study, we report the 1.8 Å crystal structure of the cytoplasmic region of Alg44 in complex with dimeric self-intercalated c-di-GMP and characterize its dinucleotide-binding site using mutational analysis. The structure shows that the c-di-GMP binding region of Alg44 adopts a PilZ domain fold with a dimerization mode not previously observed for this family of proteins. Moreover, calorimetric binding analysis of residues in the c-di-GMP binding site demonstrate that mutation of Arg-17 and Arg-95 alters the binding stoichiometry between c-di-GMP and Alg44 from 2:1 to 1:1. Introduction of these mutant alleles on the P. aeruginosa chromosome show that the residues required for binding of dimeric c-di-GMP in vitro are also required for efficient alginate production in vivo. Our results suggest that the dimeric form of c-di-GMP represents the biologically active signaling molecule needed for the secretion of an important virulence factor produced by P. aeruginosa.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Characterization of a dimer preparation method for nanoscale organic aerosol

Nanoscale dimers have application in studies of aerosol physicochemical properties such as aerosol viscosity. These particle dimers can be synthesized using the dual tandem differential mobility analyzer (DTDMA) technique, wherein oppositely charged particle streams coagulate to form dimers that can be isolated using electrostatic filtration. Although some characterization of the technique has been published, a detailed thesis on the modes and theory of operation has remained outside the scope of prior work. In this paper we present new experimental data characterizing the output DTDMA size distribution and the physical processes underlying its apparent modes. Key experimental limitations for both general applications and for viscosity measurements are identified and quantified in six distinct types of DTDMA experiments. The primary consideration is the production of an adequate number of dimers, which typically requires high mobility-selected number concentration in the range 25,000-100,000 cm -3 . The requisite concentration threshold depends upon the rate of spontaneous monomer decharging, which arises predominately from interactions of the aerosol with ionizing radiation within the coagulation chamber and is instrument location dependent. Lead shielding of the coagulation chamber reduced the first-order decharging constant from ~2.0 x 10 -5 s -1 to ~0.8 x 10 -5 s -1 in our laboratory. Dimer production at monomer diameters less than 40 nm is hindered by low bipolar charging efficiency. Results from the characterization experiments shed light on design considerations for general applications and for characterization of viscous aerosol phase transitions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Ambient observations of dimers from terpene oxidation in the gas phase: Implications for new particle formation and growth: Ambient Observations of Gas-Phase Dimers

Here, we present ambient observations of dimeric monoterpene oxidation products (C 16–20 H y O 6–9 ) in gas and particle phases in the boreal forest in Finland in spring 2013 and 2014, detected with a chemical ionization mass spectrometer with a filter inlet for gases and aerosols employing acetate and iodide as reagent ions. These are among the first online dual-phase observations of such dimers in the atmosphere. Estimated saturation concentrations of 10 -15 to 10 -6 µg m -3 (based on observed thermal desorptions and group-contribution methods) and measured gas-phase concentrations of 10 -3 to 10 -2 µg m -3 (~10 6 –10 7 molecules cm -3 ) corroborate a gas-phase formation mechanism. Regular new particle formation (NPF) events allowed insights into the potential role dimers may play for atmospheric NPF and growth. The observationally constrained Model for Acid-Base chemistry in NAnoparticle Growth indicates a contribution of ~5% to early stage particle growth from the ~60 gaseous dimer compounds.

58 GEOSCIENCES↗
DOE OSTI2015

Gas-Phase Dimerization of Ethylene under Mild Conditions Catalyzed by MOF Materials Containing (bpy)Ni II Complexes

NU-1000-(bpy)Ni II , a highly porous MOF material possessing well-defined (bpy)Ni II moieties, was prepared through solvent-assisted ligand incorporation (SALI). Treatment with Et 2 AlCl affords a single-site catalyst with excellent catalytic activity for ethylene dimerization (intrinsic activity for butenes that is up to an order of magnitude higher than the corresponding (bpy)NiCl 2 homogeneous analogue) and stability (can be reused at least three times). The high porosity of this catalyst results in outstanding levels of activity at ambient temperature in gas-phase ethylene dimerization reactions, both under batch and continuous flow conditions.

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

Rotational spectra of propargyl alcohol dimer: A dimer bound with three different types of hydrogen bonds

Pure rotational spectra of the propargyl alcohol dimer and its three deuterium isotopologues have been observed in the 4 to 13 GHz range using a pulsed-nozzle Fourier transform microwave spectrometer. For the parent dimer, a total of 51 transitions could be observed and fitted within experimental uncertainty. For two mono-substituted and one bi-substituted deuterium isotopologues, a total of 14, 17, and 19 transitions were observed, respectively. The observed rotational constants for the parent dimer [A = 2321.8335(4) MHz, B = 1150.4774(2) MHz, and C = 1124.8898(2) MHz] are close to those of the most stable structure predicted by ab initio calculations. Spectra of the three deuterated isotopologues and Kraitchman analysis positively confirm this structure. Geometrical parameters and “Atoms in Molecules” analysis on the observed structure reveal that the two propargyl alcohol units in the dimer are bound by three different types of hydrogen bonds: O–H⋯O, O–H⋯π, and C–H⋯π. To the best of our knowledge, propargyl alcohol seems to be the smallest molecule forming a homodimer with three different points of contact.

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

Fibrillar dimer formation of islet amyloid polypeptides

Amyloid deposits of human islet amyloid polypeptide (hIAPP), a 37-residue hormone co-produced with insulin, have been implicated in the development of type 2 diabetes. Residues 20 – 29 of hIAPP have been proposed to constitute the amyloidogenic core for the aggregation process, yet the segment is mostly unstructured in the mature fibril, according to solid-state NMR data. Here we use molecular simulations combined with bias-exchange metadynamics to characterize the conformational free energies of hIAPP fibrillar dimer and its derivative, pramlintide. We show that residues 20 – 29 are involved in an intermediate that exhibits transient β-sheets, consistent with recent experimental and simulation results. By comparing the aggregation of hIAPP and pramlintide, we illustrate the effects of proline residues on inhibition of the dimerization of IAPP. The mechanistic insights presented here could be useful for development of therapeutic inhibitors of hIAPP amyloid formation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The dimeric form of bacterial l ‐asparaginase YpAI is fully active

l ‐asparaginases from mesophilic bacteria (ASNases), including two enzymes very successfully used in the treatment of leukaemia, have been consistently described as homotetramers. On the contrary, structural studies show that homodimers of these enzymes should be sufficient to carry out the catalytic reaction. In this report, we investigated whether the type I Yersinia pestis asparaginase (YpAI) is active in a dimeric form or whether the tetrameric quaternary structure is critical for its activity. Using multiple biophysical techniques that investigate enzymatic properties and quaternary structure at either high or low protein concentration, we found that dimeric YpAI is fully active, suggesting that the tetrameric form of this subfamily of enzymes does not bear significant enzymatic relevance. In this process, we extensively characterized YpAI, showing that it is a cooperative enzyme, although the mechanism of allostery is still not definitely established. We showed that, like most type I ASNases, the substrate affinity of YpAI is low and this enzyme is very similar in terms of both the structure and enzymatic properties to homologous type I ASNase from Escherichia coli (EcAI). We extended these studies to more medically relevant type II ASNases, used as anti‐leukaemia drugs. We confirmed that type II ASNases are not allosteric, and that they might also be functional in a dimeric form. However, the determination of the accurate tetramer⇆dimer dissociation constants of these enzymes that most likely lie in the picomolar range is not possible with currently available biophysical techniques.

Biochemistry & Molecular Biology↗
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 OSTI2022

Triangular lattice quantum dimer model with variable dimer density

Abstract Quantum dimer models are known to host topological quantum spin liquid phases, and it has recently become possible to simulate such models with Rydberg atoms trapped in arrays of optical tweezers. Here, we present large-scale quantum Monte Carlo simulation results on an extension of the triangular lattice quantum dimer model with terms in the Hamiltonian annihilating and creating single dimers. We find distinct odd and even $${{\mathbb{Z}}}_{2}$$ Z 2 spin liquids, along with several phases with no topological order: a staggered crystal, a nematic phase, and a trivial symmetric phase with no obvious broken symmetry. We also present dynamic spectra of the phases, and note implications for experiments on Rydberg atoms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Simulations of cellulose translocation in the bacterial cellulose synthase suggest a regulatory mechanism for the dimeric structure of cellulose

The processive cycle of the bacterial cellulose synthase (Bcs) includes the addition of a single glucose moiety to the end of a growing cellulose chain followed by the translocation of the nascent chain across the plasma membrane. The mechanism of this translocation and its precise location within the processive cycle are not well understood. In particular, the molecular details of how a polymer (cellulose) whose basic structural unit is a dimer (cellobiose) can be constructed by adding one monomer (glucose) at a time are yet to be elucidated. Here, we have utilized molecular dynamics simulations and free energy calculations to the shed light on these questions. We find that translocation forward by one glucose unit is quite favorable energetically, giving a free energy stabilization of greater than 10 kcal mol-1. In addition, there is only a small barrier to translocation, implying that translocation is not rate limiting within the Bcs processive cycle (given experimental rates for cellulose synthesis in vitro). Perhaps most significantly, our results also indicate that steric constraints at the transmembrane tunnel entrance regulate the dimeric structure of cellulose. Namely, when a glucose molecule is added to the cellulose chain in the same orientation as the acceptor glucose, the terminal glucose freely rotates upon forward motion, thus suggesting a regulatory mechanism for the dimeric structure of cellulose. We characterize both the conserved and non-conserved enzyme-polysaccharide interactions that drive translocation, and find that 20 of the 25 residues that strongly interact with the translocating cellulose chain in the simulations are well conserved, mostly with polar or aromatic side chains. Our results also allow for a dynamical analysis of the role of the so-called 'finger helix' in cellulose translocation that has been observed structurally. Taken together, these findings aid in the elucidation of the translocation steps of the Bcs processive cycle and may be widely relevant to polysaccharide synthesizing or degrading enzymes that couple catalysis with chain translocation.

09 BIOMASS FUELS↗