Multiplexed hybridizations of positively charge-tagged peptide nucleic acids detected by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Peptide nucleic acid (PNA) is a novel class of DNA analogues in which the entire sugar-phosphate backbone is replaced by a pseudopeptide counterpart. Owing to its neutral character and the consequent lack of electrostatic repulsion, PNA exhibits very stable heteroduplex formation with complementary nucleic acid that is essentially ionic strength independent and enables hybridization under minimum salt conditions. This feature as well as its superior ion stability and easy ionization compared to DNA renders PNA very attractive for hybridization-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) applications. We have developed an approach to DNA characterization that takes advantage of multiplexed PNA hybridizations analyzed by MALDI-TOFMS. Our motivation was the further development of oligonucleotide fingerprinting, an efficient technique for cDNA and genomic DNA library characterization. Through positive 'charge-tagging' of PNA the efficiency of detection in MALDI-TOFMS was considerably enhanced permitting an unparalleled degree of multiplexing. Results from the simultaneous hybridization of 21 charge-tagged PNA hexamer oligonucleotides showed that genomic DNA and cDNA clones are successfully characterized on the basis of their hybridization profiles. The degree of multiplexing achieved may render a significant increase in throughput and hence efficiency of oligonucleotide fingerprinting possible.     

Synthesis and Evaluation as Glycosidase Inhibitors of Isoquinuclidines Mimicking a Distorted β‐Mannopyranoside

Racemic and enantiomerically pure manno‐configured isoquinuclidines were synthesized and tested as glycosidase inhibitors. The racemic key isoquinuclidine intermediate was prepared in high yield by a cycloaddition (tandem Michael addition/aldolisation) of the 3‐hydroxy‐1‐tosyl‐pyridone 10 to methyl acrylate, and transformed to the racemic N‐benzyl manno‐isoquinuclidine 2 and the N‐unsubstituted manno‐isoquinuclidine 3 (twelve steps; ca. 11% from 10 ). Catalysis by quinine of the analogous cycloaddition of 10 to (?)‐8‐phenylmenthyl acrylate provided a single diastereoisomer in high yield, which was transformed to the desired enantiomerically pure D ‐manno‐isoquinuclidines (+)‐ 2 and (+)‐ 3 (twelve steps; 23% from 10 ). The enantiomers (?)‐ 2 and (?)‐ 3 were prepared by using a quinidine‐promoted cycloaddition of 10 to the enantiomeric (+)‐8‐phenylmenthyl acrylate. The N‐benzyl D ‐manno‐isoquinuclidine (+)‐ 2 is a selective and slow inhibitor of snail β‐mannosidase. Its inhibition strength and type depends on the pH (at pH 4.5: K_i=1.0 μM , mixed type, α=1.9; at pH 5.5: K_i=0.63 μM , mixed type, α=17). The N‐unsubstituted D ‐manno‐isoquinuclidine (+)‐ 3 is a poor inhibitor. Its inhibition strength and type also depend on the pH (at pH 4.5: K_i=1.2?10³ μM , mixed type, α=1.1; at pH 5.5: K_i=0.25?10³ μM , mixed type, α=11). The enantiomeric N‐benzyl L ‐manno‐isoquinuclidine (?)‐ 2 is a good inhibitor of snail β‐mannosidase, albeit noncompetitive (at pH 4.5: K_i=69 μM ). The N‐unsubstituted isoquinuclidine (?)‐ 2 is a poor inhibitor (at pH 4.5: IC₅₀=7.3?10³ μM ). A comparison of the inhibition by the pure manno‐isoquinuclidines (+)‐ 2 and (+)‐ 3 , (+)‐ 2 /(?)‐ 2 1 : 1, and (+)‐ 3 /(?)‐ 3 1 : 1 with the published data for racemic 2 and 3 led to a rectification of the published data. The inhibition of snail β‐mannosidase by the isoquinuclidines 2 and 3 suggests that the hydrolysis of β‐D ‐mannopyranosides by snail β‐mannosidase proceeds via a distorted conformer, in agreement with the principle of stereoelectronic control.     

Synthesis and Characterization of Ge(II), Sn(II), and Pb(II) Monoamides with -NH2 Ligands

The synthesis and characterization of the first divalent germanium, tin, and lead monoamide derivatives of the parent amide group -NH(2) are presented. They have the general formula (ArMNH(2))(2) (M = Ge, Ar = Ar'(C(6)H(3)-2,6-Pr(i)(2)) or Ar* (C(6)H(3)-2,6(C(6)H(2)-2,4,6-Pr(i)(3))); M = Sn, Ar = Ar*; M = Pb, Ar = Ar*). For germanium and tin, they were obtained by reacting the corresponding terphenyl halides of the group 14 elements with liquid ammonia in diethyl ether. The lead amide derivative (Ar*PbNH(2))(2) was synthesized by reaction of LiNH(2) with Ar*PbBr in diethyl ether. The compounds were characterized by IR and multinuclear NMR spectroscopies and by X-ray crystallography in the case of the (Ar'GeNH(2))(2) or (Ar*SnNH(2))(2) derivatives. They possess dimeric structures with two -NH(2) groups bridging the germanium and tin centers. For lead, the reaction with ammonia led to isolation of a stable ammine complex of formula Ar*PbBr(NH(3)) which was characterized by IR and NMR spectroscopies and by X-ray crystallography. It is the first structural characterization of a divalent lead ammine complex.     

Vibrational structure of endohedral fullerene Sc3N@C78 (D3h'): evidence for a strong coupling between the Sc3N cluster and C78 cage.

The vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) is studied by FTIR spectroscopy, Raman spectroscopy and DFT-based quantum chemical calculations. Remarkably good agreement between experimental and calculated spectra is achieved and a full assignment of the Sc(3)N-based vibrational modes is given. Significant differences in the vibrational structure of the endohedral cluster fullerene Sc(3)N@C(78) and the empty, charged C(78) (6-): 5 (D(3h)') are rationalized by the strong coupling between the Sc(3)N cluster and the fullerene cage. This coupling has its origin in a significant overlap of the Sc(3)N and C(78) molecular orbitals, and causes atomic-charge and bond-length redistributions compared to the neutral C(78) and the C(78) (6-) anion. An ionic model is not sufficient to describe the electronic, geometric and vibrational structure of the Sc(3)N@C(78) nitride cluster fullerene.     

Preparation and Crystal Structures of the Hydrous Mercury Tellurates,HgII(H4TeVIO6) and HgI2(H4TeVIO6)(H6TeVIO6)·2H2O

Single crystals of Hg^II(H₄Te^VIO₆) (colourless to light‐yellow, rectangular plates) and Hg^I₂(H₄Te^VIO₆)(H₆Te^VIO₆)·2H₂O (colourless, irregular) were grown from concentrated solutions of orthotelluric acid, H₆TeO₆, and respective solutions of Hg(NO₃)₂ and Hg₂(NO₃)₂. The crystal structures were solved and refined from single crystal diffractometer data sets (Hg^II(H₄Te^VIO₆): space group Pna2₁, Z = 4, a =10.5491(17), b = 6.0706(9), c = 8.0654(13)Å, 1430 structure factors, 87 parameters, R[F² > 2σ(F²)] = 0.0180; Hg^I₂(H₄Te^VIO₆)(H₆Te^VIO₆)·2H₂O: space group P1¯, Z = 1, a = 5.7522(6), b = 6.8941(10), c = 8.5785(10)Å, α = 90.394(8), β = 103.532(11), γ = 93.289(8)°, 2875 structure factors, 108 parameters, R[F² > 2σ(F²)] = 0.0184). The structure of Hg^II(H₄Te^VIO₆) is composed of ribbons parallel to the b axis which are built of [H₄TeO₆]^2— anions and Hg²⁺ cations held together by two short Hg—O bonds with a mean distance of 2.037Å. Interpolyhedral hydrogen bonding between neighbouring [H₄TeO₆]^2— groups, as well as longer Hg—O bonds between Hg atoms of one ribbon to O atoms of adjacent ribbons lead, to an additional stabilization of the framework structure. Hg^I₂(H₄Te^VIO₆)(H₆Te^VIO₆)·2H₂O is characterized by a distorted hexagonal array made up of [H₄TeO₆]^2— and [H₆TeO₆] octahedra which spread parallel to the bc plane. Interpolyhedral hydrogen bonding between both building units stabilizes this arrangement. Adjacent planes are stacked along the a axis and are connected by Hg₂²⁺ dumbbells (d(Hg—Hg) = 2.5043(4)Å) situated in‐between the planes. Additional stabilization of the three‐dimensional network is provided by extensive hydrogen bonding between interstitial water molecules and O and OH‐groups of the [H₄TeO₆]^2— and [H₆TeO₆] octahedra. Upon heating Hg^I₂(H₄Te^VIO₆)(H₆Te^VIO₆)·2H₂O decomposes into TeO₂ under formation of the intermediate phases Hg^II₃Te^VIO₆ and the mixed‐valent Hg^IITe^IV/VI₂O₆.     

A new palladium catalyst system for the cyanation of aryl chlorides with K4[Fe(CN)6]

The development of a novel Pd-catalyzed synthesis of (hetero)aromatic nitriles from the corresponding aryl chlorides and potassium hexacyanoferrate(II) is described. This novel protocol avoids the use of highly toxic alkali cyanides and proceeds in the presence of small amounts of palladium catalysts. High yields and selectivities of the corresponding aryl nitriles were achieved applying di(1-adamantyl)-1-butylphosphine (cataCXium^® A) as the ligand.     

Electronic influences on 3J(C,H) coupling constants via -S-, -S(O)- and -SO2-: their determination, calculation and comparison of detection methods

3J(C,H) coupling constants via a sulfur atom in two series of compounds, both including a sulfide, a sulfoxide and a sulfone, were detected experimentally and calculated by quantum mechanical methods. In the first series (1-3) the coupling between a hydrogen, bonded to an sp3 carbon, and an sp2 carbon is treated; the second series (4-6) deals with the coupling between a hydrogen, bonded to an sp3 carbon, and an sp3 carbon. Different pulse sequences (broadband HMBC, SelJres, 1D HSQMBC, J-HMBC-2, selective J-resolved long-range experiment and IMPEACH-MBC) proved to be useful in determining the long-range 3J(C,H) coupling constants. However, the dynamic behaviour of two of the compounds (4 and 6) led to weighted averages of the two coupling constants expected (concerning equatorial and axial positions of the corresponding hydrogens). DFT calculations proved to be useful to calculate not only the 3J(C,H) coupling constants but also the different contributions of FC, PSO, DSO and SD terms; the calculation of the Fermi contact term (FC) was found to be sufficient for the correct estimation of 3J(C,H) coupling constants.     

Accurate mass measurements by Fourier transform mass spectrometry in the study of advanced glycation end products/peptides

The Maillard reaction occurring between sugars and amino groups is important in living systems. When amino groups belonging to protein chains are involved, the Maillard reaction has been invoked as responsible for protein cross-linking and the production of 'toxic' compounds. The reaction leads to the production of a heterogeneous group of substances, usually called advanced glycation end products (AGEs). Classical analytical approaches, such as spectroscopic (ultraviolet, fluorescence) and mass spectrometric (matrix-assisted laser desorption/ionization, liquid chromatography/electrospray ionization mass spectrometry) methods, have shown that the digestion mixture is highly complex. However, there are clear differences between the digestion mixtures of glycated and unglycated human serum albumin (HSA). In the former case, possible glycated peptides belonging to the AGE peptide class may be identified. Tandem mass spectrometric experiments on selected species seemed to be promising as regards structural information, but it was thought of interest to undertake the present investigation, based on liquid chromatography/electrospray ionization Fourier transform mass spectrometry, in order to obtain definitive results on their elemental composition. Using this approach, about 20 glycated peptides were detected and their possible structures were postulated by examining the known sequence of HSA.     

Ring opening of 2-(cyanomethyl)aziridines by acid chlorides: synthesis of novel 4-amino-2-butenenitrile derivatives through intermediate aziridinium salts

1-Arylmethyl-2-(cyanomethyl)aziridines were transformed into novel N-arylmethyl-N-(2-chloro-3-cyanopropyl)amides as the major reaction products upon treatment with acid chlorides in CH₂Cl₂ through the ring opening of intermediate aziridinium salts. Subsequently, N-arylmethyl-N-(2-chloro-3-cyanopropyl)amides were converted into stable N-arylmethyl-N-(3-cyano-2-propenyl)amides for the first time by means of a dehydrochlorination mediated by Et₃N in CH₂Cl₂.     

Struktur von S-9,10-Dimethyl-1,3,5,7-tetraarsa-2,4,6,8-tetraoxaadamantan und 9,10-Diethyl-1,3,5,7-tetraarsa-2,4,6,8-tetraoxaadamantan

Structure of S-9,10-Dimethyl-1,3,5,7-tetraarsa-2,4,6,8-tetraoxaadamantane and 9,10-Diethyl-1,3,5,7-tetraarsa-2,4,6,8-tetraoxaadamantane S-9,10-Dimethyl-1,3,5,7-tetraarsa-2,4,6,8-tetraoxaadamantane ( 1 ) and 9,10-diethyl-1,3,5,7-tetraarsa-2,4,6,8-tetraoxaadamantane ( 2 ) have been prepared by the reaction of propionic acid, propionic anhydride and butyric acid, butyric anhydride, respectively, with arsenic(III)-oxide. The crystals of 1 are rhombic, a = 6.902(4), b = 11.121(5), c = 13.988(8), space group P2₁2₁2₁. The crystals of 2 are monoclinic, a = 11.757(10), b = 11.255(10), c = 18.631 (18), β = 91.78(7), space group P2₁/n. The mean bond lengths and angles in 1 are AsO = 1.790 Å, AsC = 1.959 Å, OAsO = 100.60°, CAsO = 99.65°, AsOAs = 128.77°, AsCAs = 118.73°, and in 2 they are AsO = 1.780 Å, AsC = 1.978 Å, OAsO = 101.45°, CAsO = 99.55°, AsOAs = 129.64°, AsCAs = 117.72°.