Implications of active site constraints on varied DNA polymerase selectivity

DNA polymerase selectivity often varies significantly depending on the DNA polymerase. The origin of this varying error propensity is elusive. It is assumed that DNA polymerases form nucleotide binding pockets that differ in properties such as shape and tightness. We tested this prediction and studied HIV-1 RT by employment of size-augmented nucleotides and site-directed mutagenesis of the enzyme. New valuable insights into the mechanism of DNA polymerase fidelity were obtained. The presented study provides experimental evidence that variations of steric constraints within the nucleotide binding pocket of at least two DNA polymerases cause variations in nucleotide incorporation selectivity. Thus, our results support the concept of active site tightness as a causative in differential fidelity among DNA polymerases.     

Enantioselective total syntheses of manzamine a and related alkaloids

As a prelude to undertaking the total syntheses of the complex manzamine alkaloids, a series of model studies were conducted to establish the scope and limitations of intramolecular [4 + 2] cycloadditions of N-acylated vinylogous ureas with the trienic substrates 17a,b, 28a,b, and 34. These experiments clearly demonstrated that the geometry of the internal double bond and the presence of an electron-withdrawing group on the diene moiety were essential for the facile and stereoselective formation of the desired cycloadducts. The enantioselective syntheses of the manzamine alkaloids ircinol A (75), ircinal A (5), and manzamine A (1) were then completed by employing a convergent strategy that featured a novel domino Stille/Diels-Alder reaction to construct the tricyclic ABC ring core embodied in these alkaloids. Thus, the readily accessible chiral dihydropyrrole 58 was first converted in a single chemical operation into the key tricyclic intermediate 60. Two ring-closing metathesis reactions were then used to form the 13- and 8-membered rings leading to Z-72 and 74, the latter of which was quickly elaborated into ircinal A (5) via ircinol A (75). The synthetic 5 thus obtained was converted into manzamine A (1) following literature precedent. This concise synthesis of ircinal A required a total of 24 operations from commercially available starting materials with the longest linear sequence being 21 steps.     

The Dynamic Behaviour and NMR Solution structures of complexes of the type (Bisphosphine)(cycloocta-1,5-diene)iridium(I) and the X-ray crystal structure of (cycloocta-1,5-diene)((−)-norphos)iridium(I) hexafluorophosphate

A square-planar coordination geometry was found for the complex [Ir(cod){(?)-norphos}][PF₆] ( 1b [PF₆]; cod = cylcoocta-1,5-diene and (?)-norphos = [(2R,3R)-8-9-10-trinorborn-5-ene-2,3-diyl]bis(diphenylphosphine)) in the solid state by X-ray diffraction. Crystal data: monoclinic, space group P2₁, a = 10.751 (6), b = 18.669(14), c = 12.037(8) Å, β = 114.82(5)°, Z = 2. A total structural assignment including the configurational and conformational aspects of this and the related compounds [Ir(bishosphine)(cod)]X (bisphosphine = (?)-chiraphos = (2S,3S)-2,3-bis(diphenylphosphino)butane and (?)-norphos, X = Cl, CF₃SO₃, or PF₆) was carried out in solution by one- and two-dimensional NMR spectroscopy. The complexes containing the CF₃SO₃^? and PF₆^? anions are four-coordinate cations with square-planar geometry, whereas the chlorides are five-coordinate neutral compounds showing solvent-dependent dynamic behaviour. In toluene, two diastereoisomers of [IrCl(cod){(?)-norphos}] ( 2b ) exist and interconvert slowly at room temperature. This interchange is fast in CDCl₃ solution, and it is likely to involve Cl dissociation and the formation of the cation [Ir(cod){(?)-norphos}]⁺ as an intermediate.     

A Useful Modification of the Evans Auxiliary: 4-Isopropyl-5,5-diphenyloxazolidin-2-one

The 4-isopropyl-5,5-diphenyloxazolidinone ( 1 ) is readily prepared from (R)- or (S)-valine ester, PhMgBr, and ethyl chlorocarbonate. It has a melting point of ca. 250°, a low solubility in most organic solvents, and a C=O group which is sterically protected from nucleophilic attack. Thus, the soluble N-acyl-oxazolidinones ( 7 – 16 ) can be prepared from 1 with BuLi at temperatures around 0° instead of −78° (Scheme 3), their Li enolates can be generated with BuLi, rather than with LDA, and deacylation in the final step of the procedure can be achieved with NaOH at ambient temperatures (Scheme 12), with facile recovery of the precipitating auxiliary 1 (filtering, washing, and drying). The following reactions of N-acyl-oxazolidinones from 1 have been investigated: alkylations (Scheme 4), aminomethylations and hydroxymethylations (Scheme 5), aldol additions (Schemes 6 and 7), Michael additions (Schemes 9 and 10), and a (4+2) cycloaddition (Scheme 11). The well-known features of reactions following the Evans methodology (yield, diastereoselectivity, dependence on conditions, counter ions, additives etc.) prevail in these transformations. Most products, however, have higher melting points and a much more pronounced crystallization tendency than those derived from conventional oxazolidinones, and can thus be purified by recrystallization, avoiding chromatography (Table 1). The disadvantage of 1 having a higher molecular weight (ca. 150 Da) than the non-phenyl-substituted auxiliary is more than compensated by the ease of its application, especially on large scale. A number of crystal structures of oxazolidinones derived from 1 and a TiCl₄ complex of an oxazolidinone are described and discussed in view of the diastereoselective-reaction mechanisms.     

Deoxyfluorination of phenols

An operationally simple ipso fluorination of phenols with a new deoxyfluorination reagent is presented.     

Biphasic synthesis of Au@SiO2 core-shell particles with stepwise ligand exchange

We report the synthesis of well-dispersed core-shell Au@SiO(2) nanoparticles with minimal extraneous silica particle growth. Agglomeration was suppressed through consecutive exchange of the stabilizing ligands on the gold cores from citrate to L-arginine and finally (3-mercaptopropyl)triethoxysilane. The result was a vitreophilic, stable gold suspension that could be coated with silica in a biphasic mixture through controlled hydrolysis of tetraethoxysilane under L-arginine catalysis. Unwanted condensation of silica particles without gold cores was limited by slowing the transfer across the liquid-liquid interface and reducing the concentration of the L-arginine catalyst. In-situ dynamic light scattering and optical transmission spectroscopy revealed the growth and dispersion states during synthesis. The resulting core-shell particles were characterized via dynamic light scattering, optical spectroscopy, and electron microscopy. Their cores were typically 19 nm in diameter, with a narrow size distribution, and could be coated with a silica shell in multiple steps to yield core-shell particles with diameters up to 40 nm. The approach was sufficiently controllable to allow us to target a shell thickness by choosing appropriate precursor concentrations.     

Exchange coupling through diamagnetic [Fe(CO)4]2- bridging ligands in a xenophilic cluster

The electronic structure of so-called 'xenophilic' clusters, which contain both organometallic fragments and Werner-type paramagnetic transition metal centres, presents a challenge to simple theories of bonding. Density functional theory shows clearly that the cluster Mn(2)(thf)(4)(Fe(CO)(4))(2) is best described as an exchange-coupled Mn(II)(2) dimer, the closed-shell organometallic [Fe(CO)(4)](2-) fragments acting simply as bridging ligands. The high-spin configuration of the Mn(II) ions leads to single occupation of the Mn-Fe σ* orbitals and therefore substantially weaker metal-metal bonding than in conventional low-valent organometallic clusters. The transition metal fragments are effective mediators of superexchange (J(calc) = -44 cm(-1)), leading to the measured effective magnetic moment of ~5 μ(B) at 300 K, considerably lower than the limiting value of 8.37 μ(B) for two uncoupled S = 5/2 Mn(II) centres.     

Synthesis, structure, chemical stability, and electrical properties of Nb-, Zr-, and Nb-codoped BaCeO3 perovskites

We report the effect of donor-doped perovskite-type BaCeO(3) on the chemical stability in CO(2) and boiling H(2)O and electrical transport properties in various gas atmospheres that include ambient air, N(2), H(2), and wet and dry H(2). Formation of perovskite-like BaCe(1-x)Nb(x)O(3±δ) and BaCe(0.9-x)Zr(x)Nb(0.1)O(3±δ) (x = 0.1; 0.2) was confirmed using powder X-ray diffraction (XRD) and electron diffraction (ED). The lattice constant was found to decrease with increasing Nb in BaCe(1-x)Nb(x)O(3±δ), which is consistent with Shannon's ionic radius trend. Like BaCeO(3), BaCe(1-x)Nb(x)O(3±δ) was found to be chemically unstable in 50% CO(2) at 700 °C, while Zr doping for Ce improves the structural stability of BaCe(1-x)Nb(x)O(3±δ). AC impedance spectroscopy was used to estimate electrical conductivity, and it was found to vary with the atmospheric conditions and showed mixed ionic and electronic conduction in H(2)-containing atmosphere. Arrhenius-like behavior was observed for BaCe(0.9-x)Zr(x)Nb(0.1)O(3±δ) at 400-700 °C, while Zr-free BaCe(1-x)Nb(x)O(3±δ) exhibits non-Arrhenius behavior at the same temperature range. Among the perovskite-type oxides investigated in the present work, BaCe(0.8)Zr(0.1)Nb(0.1)O(3±δ) showed the highest bulk electrical conductivity of 1.3 × 10(-3) S cm(-1) in wet H(2) at 500 °C, which is comparable to CO(2) and H(2)O unstable high-temperature Y-doped BaCeO(3) proton conductors.     

Oligomeric nucleic acids as antivirals

Based on the natural functions and chemical characteristics of nucleic acids, a variety of novel synthetic drugs and tools to explore biological systems have become available in recent years. To date, a great number of antisense oligonucleotides, RNA interference-based tools, CpG?containing oligonucleotides, catalytic oligonucleotides, decoys and aptamers has been produced synthetically and applied successfully for understanding and manipulating biological processes and in clinical trials to treat a variety of diseases. Their versatility and potency make them equally suited candidates for fighting viral infections. Here, we describe the different types of nucleic acid-based antivirals, their mechanism of action, their advantages and limitations, and their future prospects.