Preparation and analysis of oligonucleotides containing the c4'-oxidized abasic site and related mechanistic probes

The C4'-oxidized abasic site (C4-AP) is produced by a variety of DNA damaging agents. This alkali labile lesion can exist in up to four diastereomeric cyclic forms, in addition to the acyclic keto-aldehyde. Synthetic oligonucleotides containing the lesion were prepared from a stable photochemical precursor. Chemical integrity of the lesion containing oligonucleotides was probed using phosphodiesterase lability. Analysis of the 3',5'-phosphate diester of the monomeric lesion released from single diastereomers of photolabile precursors by 1H NMR indicates that isomerization of the hemiacetal and/or hemiketal is rapid. The syntheses and characterization of oligonucleotides containing configurationally stable analogues of C4-AP, which serve as mechanistic probes for deciphering the structural basis of the biochemical and biological effects of the C4'-oxidized abasic lesion, are also described.     

Structure and photochemistry of 18-diazo-1,4,7,10,13,16-hexaoxacyclononadeca-17,19-dione and its sodium and potassium complexes. Control of the ground-state conformation of 2-diazo-1,3-dicarbonyl fragment via host-guest complexation

[reaction: see text] The macrocyclic 18-diazo-1,4,7,10,13,16-hexaoxacyclononadeca-17,19-dione (3-diazo-2,4-dioxo-19-crown-6, 1) readily forms complexes with potassium (2, stability constant in methanol is K(K+) = 229 +/- 25 M(-1)) and sodium ions (3, K(Na+) = 84.2 +/- 7.9 M(-1) in methanol). According to B3LYP/6-31G+(d,p) calculations and temperature-dependent 1H NMR spectroscopy, the predominant conformation of 1 has a Z,Z arrangement of the diazo and carbonyl groups. The X-ray crystal structure analysis showed that the potassium complex (2) has the same Z,Z arrangement, while the sodium analogue (2) exists in conformation with Z,E geometry of the diazodicarbonyl moiety. Direct 254 nm photolysis of diazo compounds 1-3 in methanol results in the formation of 3-methoxy-2,4-dioxo-19-crown-6 (5), the product of the insertion of corresponding alpha,alpha'-dicarbonylcarbene into the O-H bond of the solvent. The triplet-sensitized photolysis of diazomalonates 1-3 produces 2,4-dioxo-19-crown-6 (6), which is apparently formed via the triplet state of the intervening carbene.     

Metal "capture" by a heterotrimetalloligand, heterometallic d(10)-d(10) interactions, and unexpected iron-to-platinum silyl ligand migration: a combined experimental and theoretical study

The heterotrinuclear chain complex Hg[Fe{Si(OMe)(3)}(CO)(3)(dppm-P)](2) (dppm = Ph(2)PCH(2)PPh(2)) 1 which has a transoid arrangement of the phosphine donors was used as a versatile chelating metallodiphosphine ligand owing to the easy rotation of its metal core about the Fe-Hg sigma-bonds. Its reaction with the labile Pt(0) olefin complex [Pt(C(7)H(10))(3)] yielded [HgPt{Si(OMe)(3)}Fe(2)(CO)(6){Si(OMe)(3)}(mu-dppm)(2)] 5 which resulted, after coordination of the dangling phosphine donors to Pt, from an unprecedented intramolecular rearrangement involving a very rare example of silyl ligand migration between two different metal centers, and the first one in metal cluster chemistry. The major structural differences observed between the heterometallic complexes obtained from 1 and d(10) Cu(I), Pd(0), or Pt(0) precursors have been established by X-ray diffraction. The bonding situation in the silyl migrated Pt complex 5 was analyzed and compared to those in the isoelectronic, but structurally distinct complexes obtained from Cu(I) and Pd(0) precursors, [Hg{Fe[Si(OMe)(3)](CO)(3)(mu-dppm)}(2)Cu](+) (2) and [Hg{Fe[Si(OMe)(3)](CO)(3)(mu-dppm)}(2)Pd] (4), respectively, by means of extended Hückel interaction diagrams. DFT calculations then allowed the energy minima associated with the three structures to be compared for 2, 4, and 5. All three minima are in close competition for the Pd complex 4, but silyl migration is favored by approximately 10 kcal mol(-)(1) for 5, mainly due to the more electronegative character of Pt with respect to Pd.     

Cooperative hydrogen-bonding effects in a water square: a single-crystal neutron and partial atomic charges and hardness analysis study

Four isomorphous complexes of formula [M(L)(4)(H(2)O)(2)]SO(4).2H(2)O (M = Co, 1a; Ni, 1b; Cu, 1c; Zn, 1d) have been isolated and characterized by single-crystal X-ray diffraction and neutron diffraction using the quasi-Laue diffractometer VIVALDI at the Institut Laue-Langevin as well as by thermogravimetric analysis. The structures contain a discrete, strongly hydrogen-bonded water tetramer which causes a significant distortion of the metal coordination sphere in each case. Partial atomic charges and hardness analysis (PACHA) calculations reveal that the shortest hydrogen bonds are not the strongest in this constrained, cyclic solid-state structure and show that the distortion at the metal center is caused by the drive to maintain the integrity of the water tetramer. The system undergoes a disorder-order transition on slow cooling that provides insight into the nature of communication between water squares.     

Oxidation reactions of an anionic gallium(I) N-heterocyclic carbene analogue with group 16 compounds

The reactivity of an anionic gallium(I) heterocycle, [K(tmeda)][:Ga([N(Ar)C(H)]2)], Ar = C6H3Pr(i)2-2,6, towards sources of elemental chalcogens and diorgano-dichalcogenides has been investigated and comparisons drawn with the reactivity of the valence isoelectronic N-heterocyclic carbene class of ligand. The reactions of the heterocycle with N2O or (Te)PEt3 yielded the dimeric, dianionic gallium(III) complexes, [K(L)]2[(mu-E)Ga([N(Ar)C(H)]2)]2, E = O, L = tmeda; E = Te, L = THF. Treatment of [K(tmeda)][:Ga([N(Ar)C(H)]2)] with the diphenyl dichalcogenides, PhEEPh, E = Se or Te, gave the one dimensional polymer, [K[(PhSe)2Ga([N(Ar)C(H)]2)]]infinity and the monomeric complex, [K(OEt2)3][(PhTe)2Ga([N(Ar)C(H)]2)], respectively. The X-ray crystal structures of the four complexes are reported.     

Living ring-opening metathesis polymerization of norbornenes bay-functionalized perylene diimides

Ring-opening metathesis polymerization (ROMP)-derived poly(oxanorbornene imide)s bearing bay-linked mono - alkoxy -M1 and 1,7-di-alkoxy M2 functionalized perylene diimides (PDIs) were synthesized using Grubb's third ( G3 ) and Hoveyda-Grubbs second generation ( HG2 ) ruthenium-alkylidene metathesis initiators. The mono-alkoxy-derived PDI-based non-ladderphane polymer poly M1 displayed 67% to 77% of the trans olefin content in the polymer chain depending on the initiator used for the polymerization. When using the symmetrical 1,7-di-alkoxy-derived PDI-based polymer poly M2 having the ladderphane type-structure, this displayed a significant amount of cis and trans olefin contents in the polymer chains, irrespective of the type of initiators used for the polymerization. ROMP of both monomers M1 and M2 proceeded in a well-controlled manner with a linear dependence of molecular weight on the monomer/initiator ratio using G3 as initiator. Optical properties of the ladderphane-based poly M2 and non-ladderphane-based poly M1 were characterized in both solution and the film state. X-ray diffraction (XRD) analysis for all the polymers showed significant π-stacking in the thin film state with ordered molecular packing and closer values of d-spacing for both poly M1 and poly M2 . Film morphology examined by AFM elucidated homogenous smooth polymer surface for both polymers in general, but with some irregularities observed for poly M1 . In addition, CV analysis revealed both polymers could be good candidates as electron-accepting materials, with excellent film-forming ability, and thermal stability.     

Application of Natural Clinoptilolite for Ammonium Removal from Sludge Water

Sludge water (SW) arising from the dewatering of anaerobic digested sludge causes high back loads of ammonium, leading to high stress (inhibition of the activity of microorganisms by an oversupply of nitrogen compounds (substrate inhibition)) for wastewater treatment plants (WWTP). On the other hand, ammonium is a valuable resource to substitute ammonia from the energy intensive Haber-Bosch process for fertilizer production. Within this work, it was investigated to what extent and under which conditions Carpathian clinoptilolite powder (CCP 20) can be used to remove ammonium from SW and to recover it. Two different SW, originating from municipal WWTPs were investigated (SW1: c₀ = 967 mg/L NH₄-N, municipal wastewater; SW2: c₀ = 718–927 mg/L NH₄-N, large industrial wastewater share). The highest loading was achieved at 307 K with 16.1 mg/g (SW1) and 15.3 mg/g (SW2) at 295 K. Kinetic studies with different specific dosages (0.05 g_CLI/mg_NH4-N), temperatures (283–307 K) and pre-loaded CCP 20 (0–11.4 mg/g) were conducted. At a higher temperature a higher load was achieved. Already after 30 min contact time, regardless of the sludge water, a high load up to 7.15 mg/g at 307 K was reached, achieving equilibrium after 120 min. Pre-loaded sorbent could be further loaded with ammonium when it was recontacted with the SW.     

Borohydride complexes of rare earths,and their applications in various organic transformations

Borohydride complexes of the rare earths have attracted increasing interest during the last decade. This review aims to cover recent results over this period with respect to the preparation, characterization, structure, and applications in organic chemistry of this family of compounds, including inorganic and organometallic complexes. Special emphasis is made on their use for polymerization catalysis.