Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin

The two forms of transthyretin differing slightly in the tertiary structure, despite the presence of five mutations, show radically different properties in terms of susceptibility to the amyloid transformation process. These two forms of transthyretin are the object of analysis. The search for the sources of these differences was carried out by means of a comparative analysis of the structure of these molecules in their native and early intermediate stage forms in the folding process. The criterion for assessing the degree of similarity and differences is the status of the hydrophobic core. The comparison of the level of arrangement of the hydrophobic core and its initial stages is possible thanks to the application of divergence entropy for the early intermediate stage and for the final forms. It was shown that the minimal differences observed in the structure of the hydrophobic core of the forms available in PDB, turned out to be significantly different in the early stage (ES) structure in folding process. The determined values of divergence entropy for both ES forms indicate the presence of the seed of hydrophobic core only in the form resistant to amyloid transformation. In the form of aggressively undergoing amyloid transformation, the structure lacking such a seed is revealed, being a stretched one with a high content of β-type structure. In the discussed case, the active presence of water in the structural transformation of proteins expressed in the fuzzy oil drop model (FOD) is of decisive importance for the generation of the final protein structure. It has been shown that the resistant form tends to generate a centric hydrophobic core with the possibility of creating a globular structure, i.e., a spherical micelle-like form. The aggressively transforming form reveals in the structure of its early intermediate, a tendency to form the ribbon-like micelle as observed in amyloid.     

New heteroleptic bis-phenanthroline copper(I) complexes with dipyridophenazine or imidazole fused phenanthroline ligands: spectral, electrochemical, and quantum chemical studies

Two new sterically challenged diimine ligands L(1) (2,9-dimesityl-2-(4'-bromophenyl)imidazo[4,5-f][1,10]phenanthroline) and L(2) (3,6-di-n-butyl-11-bromodipyrido[3,2-a:2',3'-c]phenazine) have been synthesized with the aim to build original heteroleptic copper(I) complexes, following the HETPHEN concept developed by Schmittel and co-workers. The structure of L(1) is based on a phen-imidazole molecular core, derivatized by two highly bulky mesityl groups in positions 2 and 9 of the phenanthroline cavity, preventing the formation of a homoleptic species, while L(2) is a dppz derivative, bearing n-butyl chains in α positions of the chelating nitrogen atoms. The unambiguous formation of six novel heteroleptic copper(I) complexes based on L(1), L(2), and complementary matching ligands (2,9-R(2)-1,10-phenanthroline, with R = H, methyl, n-butyl or mesityl) has been evidenced, and the resulting compounds were fully characterized. The electronic absorption spectra of all complexes fits well with DFT calculations allowing the assignment of the main transitions. The characteristics of the emissive excited state were investigated in different solvents using time-resolved single photon counting and transient absorption spectroscopy. The complexes with ligand L(2), bearing a characteristic dppz moiety, exhibit a very low energy excited-state which mainly leads to fast nonradiative relaxation, whereas the emission lifetime is higher for those containing the bulky ligand L(1). For example, a luminescence quantum yield of about 3 × 10(-4) is obtained with a decay time of about 50 ns for C2 ([Cu(I)(nBu-phen)(L(1))](+)) with a weak influence of strong coordinating solvent on the luminescence properties. Overall, the spectral features are those expected for a highly constrained coordination cage. Yet, the complexes are stable in solution, partly due to the beneficial π stacking between mesityl groups and vicinal phenanthroline aromatic rings, as evidenced by the X-ray structure of complex C3 ([Cu(I)(Mes-phen)(L(2))](+)). Electrochemistry of the copper(I) complexes revealed reversible anodic behavior, corresponding to a copper(I) to copper(II) transition. The half wave potentials increase with the steric bulk at the level of the copper(I) ion, reaching a value as high as 1 V vs SCE, with the assistance of ligand induced electronic effects. L(1) and L(2) are further end-capped by a bromo functionality. A Suzuki cross-coupling reaction was directly performed on the complexes, in spite of the handicapping lability of copper(I)-phenanthroline complexes.     

Naphthalene-fused metallo-porphyrins--synthesis and spectroscopy

Oxidative aromatic coupling of meso-substituted porphyrins bearing one electron-rich naphthalene unit has been studied in detail. After thorough optimization of oxidant, naphthalene-fused porphyrins were prepared in high yield without contamination from chlorinated side-products using Fe(ClO(4))(3)·2H(2)O. Copper and nickel complexes were successfully transformed into π-expanded porphyrins in 40-83% yield.     

Dynamic and static behaviors of N-Z-N σ(3c-4e) (Z = S, Se, and Te) interactions: atoms-in-molecules dual functional analysis with high-resolution X-ray diffraction determination of electron densities for 2-(2-pyridylimino)-2H-1,2,4-thiadiazolo[2,3-a]pyridine

The structure of 2-(2-pyridylimino)-2H-1,2,4-thiadiazolo[2,3-a]pyridine (NSN) indicates that the molecule has a planar geometry with a linear N···S···N linkage, creating a tetracyclic structure of the formal C(2v) symmetry. To clarify the nature of the NSN σ(3c-4e) bonding, together with the related NSeN and NTeN, the dynamic and static behaviors are investigated by applying atoms-in-molecules (AIM) dual functional analysis to both the fully optimized and perturbed structures. The structures were optimized computationally, retaining C(2v) symmetry. All bond critical points are detected as expected and exhibited on both sides of the N···Z···N moiety which supports the formation of NZN σ(3c-4e). It is confirmed that N···S···N is of the covalent nature close to Me(2)S(+)-?-Cl or Me(2)Se(+)-?-Br, whereas N···Se···N and N···Te···N have the (regular) CS nature close to the CT adducts of Me(2)S(-?-Cl)(2) (TBP) and Me(2)Se-?-Br(2) (MC), respectively. An experimental high-resolution charge density determination has been performed on NSN, which thoroughly supports the theoretical results. Very similar results are obtained in the analogous pyrimidyl derivatives for N···S···N, N···Se···N, and N···Te···N. AIM dual functional analysis, as validated by experimental high-resolution charge densities, is thus confirmed to be an excellent method to elucidate the nature of these interactions.     

Complexes of lanthanide nitrates with tri tert butylphosphine oxide

Reaction of lanthanide nitrates with (t)Bu(3)PO (=L) lead to the isolation of complexes Ln(NO(3))(3)L(2)·H(2)O·nEtOH (Ln = La (1), Nd(2)), Ln(NO(3))(3)L(2)?·nEtOH (Sm(3), Eu(4)), and Ln(NO(3))(3)L(2) (Dy(5), Er(6), Lu(7)). These have been characterized by elemental analysis, infrared and NMR((1)H, (13)C and (31)P) spectroscopy and single-crystal X-ray diffraction. The structures show L to be positioned on opposite sides of the metal with the nitrates forming an equatorial band. When Ln = Dy, Er, and Lu two distinct molecules are present in the unit cell. A major isomer (70%) has a (P)O-Ln-O(P) angle of less than 180° with one of the nitrate ligands twisted out of the plane of the other nitrates while the lower abundance isomer is more symmetric with the (P)O-Ln-O(P) angle of 180° and the nitrate ligands coplanar giving a hexagonal bipyramidal geometry. These isomers cannot be observed by variable temperature solution (31)P NMR measurements but are clearly seen in the solid-state NMR spectrum of the Lu complex. Variable temperature solid-state NMR indicates that the isomers do not interconvert at temperatures up to 100 °C. Attempts to prepare cationic species [Ln(NO(3))(2)L(3)](+)[PF(6)](-) have not been totally successful and led to the isolation of crystals of Lu(NO(3))(3)L(2) and Tb(NO(3))(3)L(2).CH(3)CN (8).     

Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers

Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use.     

Semipinacol rearrangement of cis-fused β-lactam diols into keto-bridged bicyclic lactams

The 6-azabicyclo[3.2.1]octane ring system, prevalent in a range of biologically active molecules, is prepared through a novel semipinacol rearrangement utilizing a cyclic phosphorane or sulfite intermediate. The rearrangement proceeds with exclusive N-acyl group migration of a β-lactam ring and results in carbonyl functionality at the 7- and bridging 8-position of the bicycle. Precursor ring-fused β-lactam diols are prepared through a sequence of 4-exo trig carbamoyl radical cyclization, regioselective dithiocarbamate group elimination, and dihydroxylation.     

Controlled production of subradiant states of a diatomic molecule in an optical lattice

We report the successful production of subradiant states of a two-atom system in a three-dimensional optical lattice starting from doubly occupied sites in a Mott insulator phase of a quantum gas of atomic ytterbium. We can selectively produce either a subradiant 1(g) state or a superradiant 0(u) state by choosing the excitation laser frequency. The inherent weak excitation rate for the subradiant 1(g) state is overcome by the increased atomic density due to the tight confinement in a three-dimensional optical lattice. Our experimental measurements of binding energies, linewidth, and Zeeman shift confirm the observation of subradiant levels of the 1(g) state of the Yb(2) molecule.     

Neutral Nickel(II) and Copper(II) Tetraazamacrocyclic Complexes as Molecular Rods Attached to Gold Electrodes

New dithiolated derivatives of neutral Cu^II and Ni^II tetraazamacrocyclic complexes have been synthesized and characterized by spectroscopic and diffractional methods. These rod‐shaped molecules were assembled in monocomponent and mixed monolayers on gold electrodes. In the mixed monolayers, the active molecules were embedded in a hexanethiol matrix. The dithiolated complexes are oriented perpendicularly to the electrode, and reveal faster kinetics of electron transfer than those assembled in a single‐component monolayer. They appear as protrusions, which are easily addressed by using the STM method. In the presence of a suitable electron acceptor in the solution, the donor properties of the anchored Cu complex were weakened, which revealed donor–acceptor interactions with the monolayer. The peak position in the voltammogram indicates a stronger interaction of the solution‐based acceptor with the reduced Cu^II form than with the Cu^III complex. This suggests the possibility of switching the association on or off by applying an appropriate potential.     

Intrinsic Ultracontractivity for Stable Semigroups on Unbounded Open Sets

We study the intrinsic ultracontractivity of the semigroup of the isotropic stable process on an unbounded open set. A two-sided estimate of the first eigenfunction of the semigroup is derived. We obtain general geometric conditions for intrinsic ultracontractivity which yield a necessary and sufficient condition for non-degenerate horn-shaped sets. The research was supported by KBN grant 1 P03A 020 28.