Sonochemical synthesis, optical properties and DFT studies on novel (N-arylamino)phenothiazinium dyes suitable for fluorescence cells imaging.

Novel (N-arylamino)phenothiazinium dyes containing meta-substituted-arylamine auxochrome units were successfully obtained by applying a sonochemical protocol designed for a more efficient energy usage in the preparation of methylene blue (MB) analogues. Single crystal X-ray diffraction analysis revealed the spatial arrangement in aggregated crystalline state of (N-(meta-bromoaryl)amino)phenothiazinium dye with minor variances induced by the nature of the halogenide counterion (iodide or chloride). The optical UV-vis properties of the novel (N-arylamino)phenothiazinium dyes were comparable to those of the parent MB, with the longest wavelength absorption maxima situated in the visible range (640-680 nm), large molar extinction coefficients (log ε = 4.5-5.1) and weak solvatochromism in polar solvents. Their fluorescence emission in solid state was evidenced by One Photon Excited Fluorescence Lifetime Imaging (OPE-FLIM) and Two Photon Excited Fluorescence Lifetime Imaging (TPE-FLIM) experiments. Theoretical calculations based on Time Dependent-Density Functional Theory (TD-DFT) at B3PW91 and CAM-B3LYP/def2-SV(P) level of theory predicted absorption and fluorescence emission wavelength maxima in reasonable agreement with experimental data. Computational results suggest that the electronic excitations imply a departure from the planar molecular ground state towards geometrically rearranged excited states disfavoring the vibronic couplings due to a high degree of flexibility induced by the conformational motion of the N-arylamino auxochromes. Preliminary studies regarding the dyes' relevance in biological environment indicated lipophilicity (log P octanol/water 0.5-2.3), no aggregation tendency in diluted solutions in the concentration range 10-50 microM and ability for cytoplasmatic staining of D407 human retinal pigment epithelial cells.

The adducts of cyano- and aquacobalamin with hypochlorite.

Hypochlorite is known to oxidatively degrade the corrin ring of cobalamin. Here, transient reaction intermediates are described in the reaction of aqua as well as of cyano-cobalamin with hypochlorite, using stopped-flow UV-vis kinetics. For aqua-cobalamin, the intermediate is assigned as arising from substitution of the aqua ligand with hypochlorite. For cyano-cobalamin, the intermediate is proposed to arise from substitution of the benzimidazole ligand trans to the cyanide. In both cases, the intermediates would feature a new Co(III)-OCl-bond-which is also supported by density functional theory (DFT) calculations.

On the Origin of the Blue Color in The Iodine/Iodide/Starch Supramolecular Complex.

The nature of the blue color in the iodine-starch reaction is still a matter of debate. Some textbooks still invoke charge-transfer bands within a chain of neutral I2 molecules inside the hydrophobic channel defined by the interior of the amylose helical structure. However, the consensus is that the interior of the helix is not altogether hydrophobic-and that a mixture of I2 molecules and iodide anions reside there and are responsible for the intense charge-transfer bands that yield the blue color of the "iodine-starch complex". Indeed, iodide is a prerequisite of the reaction. However, some debate still exists regarding the nature of the iodine-iodine units inside the amylose helix. Species such as I3-, I5-, I7- etc. have been invoked. Here, we report UV-vis titration data and computational simulations using density functional theory (DFT) for the iodine/iodide chains as well as semiempirical (AM1, PM3) calculations of the amylose-iodine/iodide complexes, that (1) confirm that iodide is a pre-requisite for blue color formation in the iodine-starch system, (2) propose the nature of the complex to involve alternating sets of I2 and Ix- units, and (3) identify the nature of the charge-transfer bands as involving transfer from the Ix- σ* orbitals (HOMO) to I2 σ* LUMO orbitals. The best candidate for the "blue complex", based on DFT geometry optimizations and TD-DFT spectral simulations, is an I2-I5-I2 unit, which is expected to occur in a repetitive manner inside the amylose helix.

Adduct of Aquacobalamin with Hydrogen Peroxide.

Aquacobalamin binds hydrogen peroxide reversibly to form a cobalt(III) hydroperoxo adduct with a 0.25 mM dissociation constant, as evidenced by UV-vis absorption spectroscopy and corroborated by NMR, Raman spectroscopy, stopped-flow UV-vis measurements, and density functional theory calculations.

Importance of the iron-sulfur component and of the siroheme modification in the resting state of sulfite reductase.

The active site of sulfite reductase (SiR) consists of an unusual siroheme-Fe4S4 assembly coupled via a cysteinate sulfur, and serves for multi-electron reduction reactions. Clear explanations have not been demonstrated for the reasons behind the choice of siroheme (vs. other types of heme) or for the single-atom coupling to an Fe4S4 center (as opposed to simple adjacency or to coupling via chains consisting of more than one atom). Possible explanations for these choices have previously been invoked, relating to the control of the spin state of the substrate-binding (siro)heme iron, modulation of the trans effect of the (Fe4S4-bound) cysteinate, or modulation of the redox potential. Reported here is a density functional theory (DFT) investigation of the structural interplay (in terms of geometry, molecular orbitals and magnetic interactions) between the siroheme and the Fe4S4 center as well as the importance of the covalent modifications within siroheme compared to the more common heme b, aiming to verify the role of the siroheme modification and of the Fe4S4 cluster at the SiR active site, with focus on previously-formulated hypotheses (geometrical/sterics, spin state, redox and electron-transfer control). A calibration of various DFT methods/variants for the correct description of ground state spin multiplicity is performed using a set of problematic cases of bioinorganic Fe centers; out of 11 functionals tested, M06-L and B3LYP offer the best results - though none of them correctly predict the spin state for all test cases. Upon examination of the relative energies of spin states, reduction potentials, energy decomposition (electrostatic, exchange-repulsion, orbital relaxation, correlation and dispersion interactions) and Mayer bond indices in SiR models, the following main roles of the siroheme and cubane are identified: (1) the cubane cofactor decreases the reduction potential of the siroheme and stabilizes the siroheme-cysteine bond interaction, and (2) the siroheme removes the quasi-degeneracy between the intermediate and high-spin states found in ferrous systems by preserving the latter as ground state; the higher-spin preference and the increased accessibility of multiple spin states are likely to be important in selective binding of the substrate and of the subsequent reaction intermediates, and in efficient changes in redox states throughout the catalytic cycle.

Why does sulfite reductase employ siroheme?

Sulfite reductase (SiR) contains in the active site a unique assembly of siroheme and a [4Fe4S] cluster, linked by a cysteine residue. Siroheme is a doubly reduced variant of heme that is not used for a catalytic function in any other enzyme. We have used non-equilibrium Green's function methods coupled with density functional theory computations to explain why SiR employs siroheme rather than heme. The results show that direct, through vacuum, charge-transfer routes are inhibited when heme is replaced by siroheme. This ensures more efficient channelling of the electrons to the catalytic iron during the six-electron reduction of sulfite to sulfide, limiting potential side-reactions that could occur if the incoming electrons were delocalized onto the macrocyclic ring.

Cationic gold clusters with eight valence electrons: possible spherical aromatic systems with Sigma holes.

The energetically preferred structures of the gold clusters Au9+, Au113+, and Au124+ with eight skeletal electrons have been studied by density functional theory for comparison with the 8-electron Au102+ cluster shown previously to have a highly favored Td tetracapped octahedral structure. The low-energy structures for the Au9+ and Au113+ clusters are found to be similar relatively spherical polyhedra. Such systems can be considered to exhibit spherical aromaticity in accord with their filled 1S21P6 shells, their diatropic NICS(0) values ranging from -21.4 to -44.3 ppm, and their shielding cone surfaces. However, the preferred spherical polyhedra for Au9+ and Au113+ are not the same as the closo deltahedra found in the BnHn2- borane dianions. Instead they have smaller internal cavities formed by capping faces of smaller deltahedra or by formation of internal Au-Au bonds. The lowest energy Au124+ structures are not similar nearly spherical polyhedral structures. Instead they are derived from planar gold subclusters by adding more gold atoms to form tetrahedral Au4 bubbles. The planar origin of the low-energy Au124+ structures relates to the energetic preference for neutral Au<14 clusters for planar structures or nearly planar structures containing small polyhedral bubbles. The presence of σ-holes has been identified on the surfaces of the complete series of the Aun(n-8)+ (n = 9 to 12) clusters. The strength of their electrostatic interactions is predicted to increase upon increasing cluster size.

Dimetallaborane analogues of the octaboranes of the type Cp2M2B6H10: structural variations with changes in the skeletal electron count.

The structures and energetics of the complete series of hydrogen-rich dimetallaboranes Cp2M2B6H10 and Cp*2M2B6H10 (Cp = η(5)-C5H5; Cp* = η(5)-Me5C5; M = Pd, Pt; Rh, Ir; Ru, Os; Re; Mo, W; Ta), including the experimentally known Cp*2Rh2B6H10 and Cp*2W2B6H10 (Cp* = η(5)-Me5C5), have been investigated by density functional theory. The lowest energy structures of the hyperelectronic Cp2M2B6H10 (M = Pd, Pt; Rh, Ir) systems have central M2B6 frameworks with a hexagonal open face similar to the B8 networks in arachno-B8H14 and nido-B8H12. The two lowest energy structures for Cp2Rh2B6H10 and Cp*2Rh2B6H10, lying within 1 kcal mol(-1) of energy, differ only in the locations of the bridging hydrogen atoms around the hexagonal hole consistent with the experimentally observed fluxionality of the hydrogen atoms in Cp*2Rh2B6H10. Most of the lowest energy Cp2M2B6H10 (M = Ru, Os) structures also have a central M2B6 framework similar to B8H12, typically with such additional features as an additional metal-metal bond or a formal metal-metal double bond. A common motif for the low-energy structures of the hypoelectronic Cp2M2B6H10 (M = Re; Mo, W; Ta) systems, including the experimentally known Cp*2W2B6H10, is a central M2B4 octahedron with its two M2B faces capped by the remaining boron atoms and with four M-B edges bridged by hydrogen atoms. Such structures can also be considered as oblatonido structures derived from the experimentally known 9-vertex oblatocloso Cp*2Re2B7H7 structure by removal of the unique degree 4 vertex atom.

Dimetallaborane analogues of pentaborane.

The structures of five-vertex dimetallaboranes Cp2M2B3H7 (Cp = η(5)-C5H5) of the second and third row transition metals, including the experimentally known Cp*2Rh2B3H7 (Cp* = η(5)-Me5C5), have been investigated by density functional theory. The predicted low-energy structures for Cp2M2B3H7 (M = Rh, Ir) are tetragonal pyramids similar to Cp*2Rh2B3H7 and pentaborane-9 B5H9 and consistent with their 14 Wadean skeletal electrons. Two Cp*2Rh2B3H7 structures with the same central Rh2B3 tetragonal prism are found with energies within ∼1 kcal mol(-1) of each other, consistent with the experimental observation of two isomers in solution. The electron-richer Cp2M2B3H7 (M = Pd, Pt) systems having 16 Wadean skeletal electrons are predicted to exhibit more open structures analogous to the known structure for the valence isoelectronic pentaborane-11 B5H11. Trigonal bipyramids with the metal atoms at equatorial vertices are typically found to be low-energy structures for the hypoelectronic Cp2M2B3H7 systems (M = Ru, Os, Re, Mo, W, Ta). In addition, the low-energy Cp2Re2B3H7 structures of the rhenium derivatives Cp2Re2B3H7 provide examples of structures based on a central Re2B2 tetrahedron with the Re-Re edge bridged by the third boron atom. Such structures can be derived from a trigonal bipyramid by the rupture of one of the axial-equatorial edges.