Isochores merit the prefix 'iso'

The isochore concept in the human genome sequence was challenged in an analysis by the International Human Genome Sequencing Consortium (IHGSC). We argue here that a statement in the IHGSC's analysis concerning the existence of isochores is misleading, because the homogeneity was not examined at a large enough length scale and consequently an inappropriate statistical test was applied. A test of the existence of isochores should be equivalent to a test of homogeneity or equality of windowed GC%. The statistical test applied in the IHGSC's analysis, the binomial test, is a test of whether individual bases are independent and identically-distributed (iid). For testing the existence of isochores, or homogeneity in windowed GC%, we propose to use another statistical test: the analysis of variance (ANOVA). It can be shown that DNA sequences that are rejected by the binomial test may not be rejected by the ANOVA test.     

Functional tuning of nucleic acids by chemical modifications: tailored oligonucleotides as drugs,devices, and diagnostics

Chemical modifications of nucleic acids present vast opportunities for extending the functions and properties of these biomolecules. In general, efforts invested in this direction pertain to the introduction of reactive functional groups for further derivatizations of oligonucleotides with numerous reporter groups and for equipping nucleic acids with catalytic chemical moieties. This review deals with representative chemical modifications in the nucleobases, sugars, and the phosphate ester backbone and their application from novel catalytic RNA selection to nucleic acid-based biosensors.     

Rearrangements of pyrrole and indole substituted enol esters of cyclohexane-1,3-dione

Enol esters 3a and 3b , from cyclohexane-1,3-dione and pyrrole-2-carbonyl chloride and indole-2-carbonyl chloride, respectively, rearranged in the presence of triethylamine to the enamino acids 7 and 12 . In the presence of cyanide, 3b , also underwent the expected rearrangement to 4b , whereas only 7 was formed from 3a . Treatment of 7 with mercuric acetate in hot acetic acid resulted in decarboxylation and aromatization to phenol 9 .     

Tandem Pummerer-Diels-Alder Reaction Sequence. A Novel Cascade Process for the Preparation of 1-Arylnaphthalene Lignans

The alpha-thiocarbocation generated from the Pummerer reaction of an o-benzoyl-substituted sulfoxide is intercepted by the adjacent keto group to produce an alpha-thio isobenzofuran as a transient intermediate which undergoes a subsequent Diels-Alder cycloaddition with added dienophiles. Acid-catalyzed ring-opening of the cycloadduct followed by aromatization gave an arylnaphthalene derivative. With acetylenic dienophiles, the tandem cyclization-cycloaddition sequence provided tetralones which result from a pinacol-type rearrangement of the primary cycloadducts. The versatility of the approach is highlighted through the synthesis of taiwanin C and E and justicidin E. The alpha-thiocarbocation generated from the Pummerer reaction of benzo[1,3]dioxol-5-yl-[6-[(ethylsulfinyl)methyl]benzo[1,3]dioxol-5-yl)methanone is intercepted by the adjacent keto group to produce an alpha-thioisobenzofuran as a transient intermediate which undergoes a subsequent Diels-Alder cycloaddition with dimethyl maleate. The initially formed Diels-Alder cycloadduct was readily converted to 5-benzo[1,3]dioxol-5-yl-8-(ethylthio)naphtho[2,3-d][1,3]dioxole-6,7-dicarboxylic acid dimethyl ester by loss of water on treatment with p-toluenesulfonic acid. Desulfurization of the thionaphthalene with Ra/Ni followed by hydrolysis of the less hindered methyl ester afforded 5-benzo[1,3]dioxol-5-ylnaphtho[2,3-d][1,3]dioxole-6,7-dicarboxylic acid 6-methyl ester which was further transformed into taiwanin C and justicidin E in good yield. Oxidation of the initial Diels-Alder cycloadduct with NaIO(4) in the presence of RuCl(3) followed by extrusion of ethyl sulfinate gave a naphthol derivative which can be converted into taiwanin E.     

Water-Soluble Phosphines. 6.(1) Tailor-Made Syntheses of Chiral Secondary and Tertiary Phosphines with Sulfonated Aromatic Substituents: Structural and Quantum Chemical Studies

Chiral water-soluble secondary phosphines (2-6) were obtained by nucleophilic phosphination of FC(6)H(4)-4-SO(3)K (1a), FC(6)H(3)-2,4-(SO(3)K)(2) (1b), and FC(6)H(4)-2-SO(3)K (1c) with RPH(2) (R = Ph, 2,4,6-Me(3)C(6)H(2), 2,4,6-iPr(3)C(6)H(2)) in the superbasic medium DMSO/KOH by employing steric control of substitution at phosphorus by bulky substituents R and sulfonic groups in the ortho position of the aromatic ring systems in 1b or 1c. The secondary phosphines may be deprotonated in DMSO/KOH to give phosphido anions which on reaction with alkyl halides (PhCH(2)Cl, Br(CH(2))(3)Br, and C(12)H(25)Br) yield mono- or bidentate tertiary phosphines (7-10). Ligands of this type are alternatively accessible by nucleophilic arylation of secondary phosphines, e.g. Ph(Me)PH or Ph(H)P(CH(2))(3)P(H)Ph with 1a or 1b, respectively. The crystal structure of the starting material 1b.H(2)O (space group P2(1)/m) has been determined. In the solid state of 1b.H(2)O the individual molecules are interconnected by ionic interactions between the potassium cations and the SO(3)(-) anions. The C-F bond (C(1)-F 1.347(4) ?) is shorter than that in C(6)H(5)F (1.356(4) ?). The unit cell of 7a.0.5H(2)O (space group P&onemacr;), the first structurally characterized chiral phosphine with a sulfonated phenyl substituent, contains the two enantiomers. Due to the asymmetrical substitution at phosphorus the PC(3) skeletons are significantly distorted (P(1)-C(1,11,31) 1.864(10), 1.825(8), 1.841(7) ?). The electronic structure of sulfonated fluorobenzenes FC(6)H(5)(-)(n)()(SO(3)M)(n)() (M = K, NH(4), n = 1-3) is discussed on the basis of quantum chemical calculations. In particular, the reactivity difference toward nucleophilic phosphination within the series is rationalized in terms of steric factors and of the -I effect of the sulfonic groups.     

Modeling the chemistry of plasma polymerization using mass spectrometry

The goal of the project is a solvent free painting shop. The environmental technologies laboratory is developing processes of plasma etching and polymerization. Polymerized thin films are first-order corrosion protection and primer for painting. Using pure acetylene we get very nice thin films which were not bonded very well. By using air as bulk gas it is possible to polymerize, in an acetylene plasma, well bonded thin films which are stable first-order corrosion protections and good primers. UV/Vis spectroscopy shows nitrogen oxide radicals in the emission spectra of pure nitrogen and air. But nitrogen oxide is fully suppressed in the presence of acetylene. IR spectroscopy shows only C=O, CH(2) and CH(3) groups but no nitrogen species. With the aid of UV/Vis spectra and the chemistry of ozone formation it is possible to define reactive traps and steps, molecule depletion and processes of proton scavenging and proton loss. Using a numerical model it is possible to evaluate these processes and to calculate theoretical mass spectra. Adjustment of theoretical mass spectra to real measurements leads to specific channels of polymerization which are driven by radicals especially the acetyl radical. The estimated theoretical mass spectra show the specific channels of these chemical processes. It is possible to quantify these channels. This quantification represents the mass flow through this chemical system. With respect to these chemical processes it is possible to have an idea of pollutant production processes.     

Geometric H/D isotope effects and cooperativity of the hydrogen bonds in porphycene.

We investigate the primary, secondary, and vicinal hydrogen/deuterium (H/D) isotope effects on the geometry of the two intramolecular hydrogen bonds in porphycene. Multidimensional potential energy surfaces describing the anharmonic motion in the vicinity of the trans isomer are calculated for the different symmetric (HH/DD) and asymmetric (HD) isotopomers. From the solution of the nuclear Schr?dinger equation the ground-state wavefunction is obtained, which is further used to determine the quantum corrections to the classical equilibrium geometries of the hydrogen bonds and thus the geometric isotope effects. In particular, it is found that the hydrogen bonds are cooperative, that is, both expand simultaneously even in the case of an asymmetric isotopic substitution. The theoretical predictions compare favorably with NMR chemical-shift data.     

Microwave accelerated aza-Claisen rearrangements

The microwave-assisted thermal aza-Claisen rearrangement of allylic imidates and thiocyanates to the corresponding amides and isothiocyanates is investigated. Significant accelerations of the rearrangement of allylic imidates to amides and of allylic thiocyanates to isothiocyanates in comparison with standard thermal reactions is observed.     

Tandem asymmetric conjugate addition--silylation of enantiomerically enriched zinc enolates. Synthetic importance and mechanistic implications

[formula: see text] The zinc enolates, resulting from the copper-catalyzed enantioselective conjugate addition of dialkyl zinc reagents to cyclic and acyclic enones, could be trapped, quantitatively, as silyl enol ethers with TMSOTf in apolar solvents or with TMSCI and NEt3. These enantiomerically enriched silyl enol ethers were submitted to four synthetic transformations to show their synthetic utility. The zinc enolates obtained from acyclic enones were found to be configurationally stable, as shown by the stereochemistry of the silyl enol ethers.