Search results for "dimer"
showing 10 items of 558 documents
Mahler Measuring the Genetic Code of Amoebae
2023
Amoebae from tropical geometry and the Mahler measure from number theory play important roles in quiver gauge theories and dimer models. Their dependencies on the coefficients of the Newton polynomial closely resemble each other, and they are connected via the Ronkin function. Genetic symbolic regression methods are employed to extract the numerical relationships between the 2d and 3d amoebae components and the Mahler measure. We find that the volume of the bounded complement of a d-dimensional amoeba is related to the gas phase contribution to the Mahler measure by a degree-d polynomial, with d = 2 and 3. These methods are then further extended to numerical analyses of the non-reflexive Ma…
Light-induced Changes in the Dimerization Interface of Bacteriophytochromes
2015
Phytochromes are dimeric photoreceptor proteins that sense red light levels in plants, fungi, and bacteria. The proteins are structurally divided into a light-sensing photosensory module consisting of PAS, GAF, and PHY domains and a signaling output module, which in bacteriophytochromes typically is a histidine kinase (HK) domain. Existing structural data suggest that two dimerization interfaces exist between the GAF and HK domains, but their functional roles remain unclear. Using mutational, biochemical, and computational analyses of the Deinococcus radiodurans phytochrome, we demonstrate that two dimerization interfaces between sister GAF and HK domains stabilize the dimer with approximat…
N-protonated 2-pyridylnickel(II) complexes insertion of isocyanides into the nickel2-pyridyl bond
1987
The reaction of the binuclear complex [NiCl(μ-2-py)(PPh3)]2 (μ-2-py = μ-C5H4N-C2,N) with the phosphines L (L = PPh3, PMePh2, PMe2Ph or PEt3) or dppe (= 1,2-bis(diphenylphosphino)ethane) in the presence of HClO4 yields the N-protonated 2-pyridyl derivatives trans-[NiCl(2-pyH)(L)2]ClO4 or [NiCl(2-pyH)(dppe)] ClO4 (2-pyH = C5H5N-C2) with a square-planar coordination around the nickel(II) center. These products are largely associated through hydrogen bonding between the NH group and the perchlorate anion, both in the solid and in chlorinated solvents. The configuration in solution has been studied by 1H and 31P NMR spectroscopy. In the complex trans-[NiCl(2-pyH)(PMe2Ph)2]ClO4, the planar 2-pyH…
The crystal structure of 3,5-diisopropyl-4-nitropyrazole from X-ray powder diffraction data
2001
The crystal structure of 3,5-diisopropyl-4-nitropyrazole, 3c, has been determined by a Patterson Search method from laboratory X-ray powder diffraction data. The crystal data are: monoclinic symmetry with the unit-cell parameters aa 19:530O5U; ba 6:485O1U and ca 17:937O3U A; ba 100:32O1U8; space group I2/a ,C 9H15N3O2, Za 8, 293 K. After indexing the powder pattern by two methods, the unit-cell parameters found were refined by a least-squares technique. A whole pattern- fitting program was used to extract the integrated intensities. The structure was solved taking a related compound as a search model and the final Rietveld refinement converged to Rwpa 0.1971 and Rpa 0.1437. The structure pr…
Topological control in the hydrogen bond-directed self-assembly of ortho-, meta-, and para-phenylene-substituted dioxamic acid diethyl esters
2010
[EN] The structures of the series of N,N¿-1,n-phenylenebis(oxamic acid ethyl ester) molecules with n = 2 (H2Et2opba, 1), 3 (H2Et2mpba, 2), and 4 (H2Et2ppba, 3) have been determined by single-crystal X-ray diffraction (XRD) methods. Density functional (DF) calculations have been performed on the simplest model system N-phenyloxamic acid methyl ester (HMepma). Compounds 1¿3 have either folded (H2Et2opba), bent (H2Et2mpba), or linear (H2Et2ppba) almost planar (periplanar) molecular configurations with the two oxalamide moieties being slightly tilted up and down, respectively, with respect to the benzene ring. The energy calculations as a function of the torsion angle (¿) around the N(amide)¿C(…
Synthesis and characterization of four novel manganese(II) chains formed by 4,4′-azobis(pyridine) and benzoate or nitrobenzoates: Stabilization of un…
2013
Abstract Four new manganese(II) coordination polymers: [Mn(4,4′-azpy)(C6H5COO)2](4,4′-azpy)0.5 (1), [Mn(4,4′-azpy)(p-(NO2)C6H4COO)2] (2), [Mn(4,4′-azpy)(m-(NO2)C6H4COO)2] (3) and [Mn(4,4′-azpy)(o-(NO2)C6H4COO)2(H2O)2] (4), where 4,4′-azpy = 4,4′-azobis(pyridine), have been synthesized by self-assembly of MnX2 (X = benzoate, p-, m-, or o-nitrobenzoates) together with 4,4′-azpy. All four complexes were characterized by elemental analyses, IR spectroscopy, thermal analyses, single-crystal X-ray diffraction analyses and variable-temperature magnetic measurements. The structural analyses reveal that complexes 1, 2 and 3 feature a 1D molecular ladder formed by syn–syn (complex 1) or syn–anti (com…
Encapsulation of Et3N+–H···OH2 in a hydrogen-bonded resorcarene capsule
2000
In the crystalline state a resorcarene dimer linked by ten hydrogen-bonding water molecules encapsulates the hydrogen-bonded complex Et3N+–H···OH2 while bromide anions are positioned outside the cavity.
ESI-FTICR investigation of triethylammonium ion-driven resorcin[4]arene dimer formation and structure
2002
In the course of mass spectrometric measurements a self-assembled hydrogen bonded resorcinarene dimer was observed, the formation of which was driven by the binding of triethylammonium ion as a guest and as an ionic label.
3-Oxa-6,8-diaza-1,2:4,5-dibenzocycloocta-1,4-dien-7-one: a three-dimensional network assembled by hydrogen-bonding, pi-pi and edge-to-face interactio…
2003
The title compound, C(13)H(10)N(2)O(2), is the first structure in which the urea moiety is incorporated into an eight-membered ring. Two molecules are found in the asymmetric unit, which are almost identical in their conformation and their hydrogen-bond pattern. The carbonyl O atom acts as a double acceptor for the NH groups of two adjacent molecules. In this way, infinite tapes are formed, which are connected via pi-pi and edge-to-face interactions in the second and third dimension. This hierarchical order of interactions is confirmed by molecular mechanics calculations. Force-field and semi-empirical calculations for a single molecule did not find the envelope conformation present in the …
Tautomerism in pyridazin-3(2H)-one: a theoretical study using implicit/explicit solvation models.
2013
Abstract The tautomeric conversion of pyridazin-3(2H)-one 1 into pyridazin-3-ol 2 has been theoretically studied using density functional theory (DFT) methods at the B3LYP/6-311++G** level. Two mechanisms have been considered for this process: (i) one in which the hydrogen is directly transferred through TS12; and (ii) another one in which a double hydrogen transfer takes place via TS1122 upon formation of the corresponding dimer. The former requires a very high activation energy of 42.64 kcal/mol as a consequence of the strain associated with the formation of the four-membered TS12, while the latter requires a much lower activation energy, 14.66 kcal/mol. Implicit, explicit, and a combinat…