G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation

G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied oligodeoxynucleotides with random bases in the loops. Sequences studied are dGGGW(i)GGGW(j)GGGW(k)GGG, with W = thymine or adenine with equal probability, and i, j, and k comprised between 1 and 4. All were studied by circular dichroism, native gel electrophoresis, UV-monitored thermal denaturation, and electrospray mass spectrometry, in the presence of 150 mM potassium, sodium, or ammonium cations. Parallel conformations are favored by sequences with short loops, but we also found that sequences with short loops form very stable multimeric quadruplexes, even at low strand concentration. Mass spectrometry reveals the formation of dimers and trimers. When the loop length increases, preferred quadruplex conformations tend to be more intramolecular and antiparallel. The nature of the cation also has an influence on the adopted structures, with K(+) inducing more parallel multimers than NH4(+) and Na(+). Structural possibilities are discussed for the new quadruplex higher-order assemblies.     

N-heterocyclic carbene complexes of Rh: reaction with dioxygen without oxidation

The reaction of oxygen with rhodium complexes containing N-heterocyclic carbenes was found to give dioxygen complexes with rare square planar geometries and unusually short O-O bond lengths. Analysis of the bonding in these complexes by Rh L-edge X-ray absorption spectroscopy (XAS), Raman spectroscopy, and DFT calculations provides evidence for a bonding model in which singlet oxygen is bound to a Rh(I) d8 metal complex, rather than the more common Rh(III) d6 peroxo species with octahedral geometry and O-O bond lengths in the 1.4-1.5 A range.     

Reactivity of an aminopyridine [LMnII]2+ complex with H2O2. Detection of intermediates at low temperature

In the present work we report the reactivity of [LMnII]2+ toward addition of hydrogen peroxide (H2O2) in acetonitrile solution, where L is a pentadentate polypyridine ligand. Formation of peroxo complexes is evidenced by low-temperature UV-visible spectroscopy, ESI-mass spectrometry, and EPR spectroscopy using parallel as well as perpendicular mode detection. The influence of the medium (basicity, water content) on the formation of various species is investigated. In basic nonanhydrous medium the fate of the reaction mixture solution is the formation of the di-mu-oxo mixed-valent Mn(III)Mn(IV) dinuclear complex. In acidic medium the building of the oxo bridges is avoided and the reaction mixture evolves toward oxidation of the ligand L. This reaction route offers new opportunities for the study of oxidation reactivity of Mn (hydro)peroxo complexes.     

Sterically congested uranyl complexes with seven-coordination of the UO2 unit: the peculiar ligation mode of nitrate in [UO2(NO3)2(Rbtp)] complexes

Addition of 1 or 2 molar equiv of Rbtp [Rbtp = 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine; R = Me, Pr ( n )] to UO 2(OTf) 2 in anhydrous acetonitrile gave the neutral compounds [UO 2(OTf) 2(Rbtp)] [R = Me ( 1), ( n )Pr ( 2)] and the cationic complexes [UO 2(Rbtp) 2][OTf] 2 [R = Me ( 3), Pr ( n ) ( 4)], respectively. No equilibrium between the mono and bis(Rbtp) complexes or between [UO 2(Rbtp) 2][OTf] 2 and free Rbtp in acetonitrile was detected by NMR spectroscopy. The crystal structures of 1 and 3 resemble those of their terpyridine analogues, and 3 is another example of a uranyl complex with the uranium atom in the unusual rhombohedral environment. In the presence of 1 molar equiv of Rbtp in acetonitrile, UO 2(NO 3) 2 was in equilibrium with [UO 2(NO 3) 2(Rbtp)] and the formation of the bis adduct was not observed, even with an excess of Rbtp. The X-ray crystal structures of [UO 2(NO 3) 2(Rbtp)] [R = Me ( 5), Pr ( n ) ( 6)] reveal a particular coordination geometry with seven coordinating atoms around the UO 2 fragment. The large steric crowding in the equatorial girdle forces the bidentate nitrate ligands to be almost perpendicular to the mean equatorial plane, inducing bending of the UO 2 fragment. The dinuclear oxo compound [U(CyMe 4btbp) 2(mu-O)UO 2(NO 3) 3][OTf] ( 7), which was obtained fortuitously from a 1:2:1 mixture of U(OTf) 4, CyMe 4btbp, and UO 2(NO 3) 2 [CyMe 4btbp = 6,6'-bis-(3,3,6,6-tetramethyl-cyclohexane-1,2,4-triazin-3-yl)-2,2'-bipyridine] is a very rare example of a mixed valence complex involving covalently bound U (IV) and U (VI) ions; its crystal structure also exhibits a seven coordinate uranyl moiety, with one bidentate nitrate group almost parallel to the UO 2 fragment. The distinct structural features of [UO 2(kappa (2)-NO 3) 2(Mebtp)], with its high coordination number and a noticeable bending of the UO 2 fragment, and of [UO 2(kappa (2)-NO 3)(kappa (1)-NO 3)(terpy)], which displays a classical geometry, were analyzed by Density Functional Theory, considering the bonding energy components and the molecular orbitals involved in the interaction between the uranyl, nitrate, and Mebtp or terpy moieties. The unusual geometry of the Mebtp derivative with the seven coordinating atoms around the UO 2 fragment was found very stable. In both the Mebtp and terpy complexes, the origin of the interaction appears to be primarily steric (Pauli repulsion and electrostatic); this term represents 62-63% of the total bonding energy while the orbital term contributes to about 37-38%.     

Water substitution on iron centers: from 0D to 1D sandwich type polyoxotungstates

Four novel polyoxotungstates have been synthesized by reaction of the sandwich type compound [Fe (III) 4(H 2O) 10(B-beta-SbW 9O 33) 2] (6-) (noted Fe 4(H 2O) 10Sb 2W 18) with ethylenediamine (en) and/or oxalate (ox) ligands under various conditions. The one-dimensional (1D) compound [enH 2] 3[Fe (III) 4(H 2O) 8(SbW 9O 33) 2].20H 2O ( 1) is isolated at 130 degrees C and results from the elimination of two water molecules and the condensation of the polyoxotungstate precursor. The reaction of Fe 4(H 2O) 10Sb 2W 18 with oxalate ligands affords the molecular complex Na 14[Fe (III) 4(ox) 4(H 2O) 2(SbW 9O 33) 2].60H 2O ( 2) where two organic ligands substitute four water molecules, while the same reaction in the presence of en molecules at 130 degrees C leads to the formation of the functionalized 1D chain [enH 2] 7[Fe (III) 4(ox) 4(SbW 9O 33) 2].14H 2O ( 3) with protonated ethylenediamine counterions. Finally, at 160 degrees C a rearrangement of the Fe 4(H 2O) 10Sb 2W 18 polyoxotungstate is observed, and the sandwich type compound [enH 2] 5[Fe (II) 2Fe (II) 2(enH) 2(Fe (III)W 9O 34) 2].24H 2O ( 4) crystallizes. In 4, the heteroelement is a Fe (III) ion, and the water molecules on the two outer Fe (II) centers are bound to pendant monoprotonated en ligands. The four compounds have been characterized by IR spectroscopy, thermogravimetric analysis, and single crystal X-ray diffraction. A detailed study of the magnetic properties of the mixed-valent hexanuclear iron complex in 4 shows evidence of an S = 5 ground-state because of spin frustration effects. A quantification of the electronic parameters characterizing the ground state ( D = +1.12 cm (-1), E/ D = 0.15) confirms that polyoxotungstate ligands induce large magnetic anisotropy.     

Triplet energy transfers in electrostatic host-guest assemblies of unsaturated organometallic cluster cations and carboxylate-containing porphyrin pigments

The unsaturated cyclic [M3(dppm)3(CO)](2+) clusters (M = Pt, Pd; dppm = Ph2PCH2PPh2; such as PF6(-) salt) exhibit a cavity formed by the six dppm-phenyl groups placed like a picket fence above the unsaturated triangular M3 dicationic center. Electrostatic interactions of the M(3+) units inside this cavity with the carboxylate anion RCO2(-) [R = tetraphenylporphyrinatozinc(II), ZnTPP; p-phenyltritolylporphyrinatozinc(II), ZnTTPP; p-phenyltritolylporphyrinatopalladium(II), PdTTPP] form dyads for through-space triplet energy transfers. The binding constants are on the order of 20,000 M(-1) in all six cases (298 K). The energy diagram built upon absorption and emission spectra at 298 and 77 K places the [Pt3(dppm)3(CO)](2+) and [Pd3(dppm)3(CO)](2+) as triplet energy donors, respectively, with respect to the ZnTPPCO2(-), ZnTTPPCO2(-), and PdTTPPCO2(-) pigments, which act as acceptors. Evidence for energy transfer is provided by the transient absorption spectra at 298 K, where triplet-triplet absorption bands of the metalloporphyrin chromophores are depicted at all time (at 298 K) with total absence of the charge-separated state in the nanosecond to microsecond time scale. Rates for energy transfer (ranging in the 10(4) s(-1) time scale) are extracted from the emission lifetimes of the [Pt3(dppm)3(CO)](2+) donor in the free chromophore and the host-guest assemblies. The emission intensity of [Pd3(dppm)3(CO)](2+) is too weak to measure its spectrum and emission lifetime in the presence of the strongly luminescent metalloporphyrin-containing materials. For the [Pd3(dppm)3(CO)](2+)...metalloporphyrin dyads, evidence for fluorescence and phosphorescence lifetime quenching of the porphyrin chromophore at 298 K is provided. These quenchings, exhibiting rates of 10(4) (triplet) and 10(8) s(-1) (singlet), are attributed to a photoinduced electron transfer from the metalloporphyrin to the cluster due to the low reduction potential.     

Syntheses, structures, and photophysical properties of mono- and dinuclear sulfur-rich gold(I) complexes

The dinuclear gold complexes [{Au(PPh 3)} 2(mu- dmid)] ( 1) ( dmid = 1,3-dithiole-2-one-4,5-dithiolate) and [{Au(PPh 3)} 2(mu- dddt)] ( 2) ( dddt = 5,6-dihydro-1,4-dithiine-2,3-dithiolate) were synthesized and characterized by X-ray crystallography. Both complexes exhibit intramolecular aurophilic interactions with Au...Au distances of 3.1984(10) A for 1 and 3.1295(11) A for 2. A self-assembly reaction between 4,5-bis(2-hydroxyethylthio)-1,3-dithiole-2-thione ( (HOCH 2 CH 2 ) 2 dmit) and [AuCl(tht)] affords the complex [AuCl{ (HOCH 2 CH 2 ) 2 dmit}] 2 ( 4), which possesses an antiparallel dimeric arrangement resulting from a short aurophilic contact of 3.078(6) A. This motif is extended into two dimensions due to intra- and intermolecular hydrogen bonds via the hydroxyethyl groups, giving rise to a supramolecular network. Three compounds were investigated for their rich photophysical properties at 298 and 77 K in 2-MeTHF and in the solid state; [Au 2(mu- dmid)(PPh 3) 2] ( 1), [Au 2(mu- dddt)(PPh 3) 2] ( 2), and [AuCl{( HOCH 2 CH 2 ) 2 dmit}] ( 4). 1 exhibits relatively long-lived LMCT (ligand-to-metal charge transfer) emissions at 298 K in solution (370 nm; tau e approximately 17 ns, where M is a single gold not interacting with the other gold atom; i.e., the fluxional C-SAuPPh 3 units are away from each other) and in the solid state (410 nm; tau e approximately 70 mus). At 77 K, a new emission band is observed at 685 nm (tau e = 132 mus) and assigned to a LMCT emission where M is representative for two gold atoms interacting together consistent with the presence of Au...Au contacts as found in the crystal structure. In solution at 77 K, the LMCT emission is also red-shifted to 550 nm (tau e approximately 139 mus). It is believed to be associated to a given rotamer. 2 also exhibits LMCT emissions at 380 nm at 298 K in solution and at 470 nm in the solid state. 4 exhibits X/MLCT emission (halide/metal to ligand charge transfer) where M is a dimer in the solid state with obvious Au...Au interactions, resulting in red-shifted emission band, and is a monomer in solution in the 10 (-5) M concentration (i.e., no Au...Au interactions) resulting in blue-shifted luminescence. Both fluorescence and phosphorescence are observed for 4.     

Homoleptic 2-mercapto benzothiazolate uranium and lanthanide complexes

Treatment of [Ln(BH 4) 3(THF) 3] (Ln = Ce, Nd) with 3 and 4 mol equiv of KSBT in tetrahydrofuran (THF) led to the formation of [Ln(SBT) 3(THF)] and [K(THF)Ln(SBT) 4], respectively. The uranium(IV) compound [U(SBT) 4(THF) 2] was obtained from U(BH 4) 4 and was reversibly reduced by sodium amalgam into the corresponding anionic uranium(III) complex. The crystal structures of [Ln(SBT) 3(THF) 2] (Ln = Ce, Nd), [K(15-crown-5) 2][Nd(SBT) 4], [U(SBT) 4(THF)], and [K(15-crown-5) 2][U(SBT) 4(py)] show the bidentate coordination mode and the thionate character of the SBT ligand.     

Generalized electronic diabatic approach to structural similarity in two‐dimensional potential energy surfaces of various topologies

Active site properties in some proteins can be affected by conformational fluctuations of neighbor residues, even when the latter are not involved directly in the binding process. A local environment thus appears to alter the relevant potential energy surface and its reaction paths. Here, some aspects of this phenomenon are simulated within a generalized electronic diabatic (GED) scheme to study the geometry and structural similarity for a class of two‐dimensional (2D) energy surfaces. The electronic quantum state is a linear superposition of diabatic basis functions, each of which is taken to represent a single (pure) electronic state for the isolated material system. Here, we describe a model reaction of isomerization by shifts in amplitudes for three diabatic species (reactant, product, and an open‐shell transition state) coupled in an external field. The “effective” 2D energy surface in the field is characterized in terms of critical points, and the amplitudes along the main reaction paths. A new feature is the introduction of a phase diagram where all possible potential‐energy‐surface topologies (consistent with three‐state systems in two linear coordinates) are matched with actual model parameters. By varying the coupling strengths between diabatic states, we classify regions of this phase diagram in terms of electronic and structural similarities; some regions comprise models whose reaction paths have geometries that belong to the catchment region of the reactant, yet are electronically akin to the diabatic transition state or product. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008