Homopolymeric pyrrolidine-amide oligonucleotide mimics: Fmoc-synthesis and DNA/RNA binding properties

By chemically modifying or replacing the backbone of oligonucleotides it is possible to modulate the DNA and RNA recognition properties and fine-tune the physiochemical properties of oligomers. This is important because it challenges our understanding of natural nucleic acid structural and recognition properties and can lead to nucleic acid mimics with a wide range of applications in nucleic acid targeting, analysis or diagnostics. In this paper we describe the solid phase synthesis of pyrrolidine-amide oligonucleotide mimics (POMs) using Fmoc-peptide chemistry. This required the synthesis of adeninyl, cytosinyl, thyminyl and guaninyl pyrrolidine monomers, with Fmoc- and standard acyl-protecting groups on the exocyclic amino groups and nucleobases respectively. These monomers were used to synthesise several thyminyl and adeninyl POM pentamers, with modest coupling efficiency. The pentamers were purified by RP-HPLC, characterised by mass spectrometry and their DNA and RNA binding properties were investigated using UV thermal denaturation/renaturation experiments. This revealed that all the pentamers exhibit strong affinity for complementary nucleic acids. The further evaluation of longer mixed-sequence POMs is described in a second accompanying paper (R. J. Worthington et al., Org. Biomol. Chem., 2006, DOI: 10.1039/b613386j).     

Preparation,NMR studies and crystal structure of mononuclear and dinuclear Pd(II) and Pt(II) complexes that contain 1,2-bis[3-(3,5-dimethyl-1-pyrazolyl)-2-thiapropyl]benzene

The reaction between 1,2-bis[3-(3,5-dimethyl-1-pyrazolyl)-2-thiapropyl]benzene (bddf) and [MCl₂(CH₃CN)₂] (M = Pd(II), Pt(II)) in a 1:1 M/L ratio in CH₂Cl₂ or acetonitrile solution, respectively, gave the complexes trans-[MCl₂(bddf)] (M = Pd(II) (1), Pt(II) (4)), and in a 2:1 M/L ratio led to [M₂Cl₄(bddf)] (M = Pd(II) (2), Pt(II) (5)). Treatment of 1 and 4 with AgBF₄ and NaBPh₄, respectively, gave the compounds [Pd(bddf)](BF₄)₂ (3) and [Pt(bddf)](BPh₄)₂ (6). When complexes 3 and 6 were heated under reflux in a solution of Et₄NBr in CH₂Cl₂/CH₃OH (1:1) for 24 h, analogous complexes to 1 and 4 with bromides instead of chlorides bonded to the metallic centre were obtained. These complexes were characterised by elemental analyses, conductivity measurements, infrared, ¹H, ¹H{¹⁹⁵Pt}, ¹³C{¹H}, ¹⁹⁵Pt{¹H} NMR, HSQC and NOESY spectroscopies. The X-ray crystal structure of the complex [Pd(bddf)](BF₄)₂ · H₂O has been determined. The metal atom is tetracoordinated by the two azine nitrogen atoms of the pyrazole rings and two thioether groups.     

Gas sensors based on nanostructured materials

Gas detection is important for controlling industrial and vehicle emissions, household security and environmental monitoring. In recent decades many devices have been developed for detecting CO(2), CO, SO(2), O(2), O(3), H(2), Ar, N(2), NH(3), H(2)O and several organic vapours. However, the low selectivity or the high operation temperatures required when most gas sensors are used have prompted the study of new materials and the new properties that come about from using traditional materials in a nanostructured mode. In this paper, we have reviewed the main research studies that have been made of gas sensors that use nanomaterials. The main quality characteristics of these new sensing devices have enabled us to make a critical review of the possible advantages and drawbacks of these nanostructured material-based sensors.     

Stereoselective preparation of six diastereomeric quatercyclopropanes from bicyclopropylidene and some derivatives

Diastereomeric meso- and d,l-bis(bicyclopropylidenyl) (5) were obtained upon oxidation with oxygen of a higher-order cuprate generated from lithiobicyclopropylidene (4) in 50 and 31 % yield, respectively. Their perdeuterated analogues meso-[D(14)]- and d,l-[D(14)]-5 were obtained along the same route from perdeuterated bicyclopropylidene [D(8)]-3 (synthesized in six steps in 7.4 % overall yield from [D(8)]-THF) in 20.5 % yield each. Dehalogenative coupling of 1,1-dibromo-2-cyclopropylcyclopropane (6) gave a mixture of all possible stereoisomers of 1,5-dicyclopropylbicyclopropylidene 16 in 69 % yield, from which (Z)-cis-16 was separated by preparative gas chromatography (26 % yield). The crystal structure of meso-5 looks like a superposition of the crystal structures of two outer bicyclopropylidene units (3) and one inner s-trans-bicyclopropyl unit, whereas the two outer cyclopropyl moieties adopt a gauche orientation with respect to the cyclopropane rings at the inner bicyclopropylidene units in (Z)-cis-16. Birch reduction with lithium in liquid ammonia of meso-5 and d,l-5 gave two pairs of diastereomeric quatercyclopropanes trans,trans-(R*,S*,R*, S*)-17/cis,trans-(R*,S*,R*,R*)-18 and trans,trans-(R*,S*,S*,R*)-19/cis,trans-(R*,S*,S*,S*)-20 in 97 and 76 % yield, respectively, in a ratio 9:1 for every pair. The latter diastereomer was also obtained as the sole product by Birch reduction of (Z)-cis-16 in 96 % yield. Under the same conditions, tetradecadeuterio analogues trans,trans-[D(14)]-(R*,S*,R*,S*)-17/cis,trans-[D(14)]-(R*, S*,R*,R*)-18 (8:1) and trans,trans-[D(14)]-(R*,S*,S*,R*)-19/cis,trans-[D(14)]-(R*,S*,S*,S*)-20 (12:1) were prepared from meso-[D(14)]-5 and d,l-[D(14)]-5 in 37 and 63 % yield, respectively. Reduction of meso-5 with diimine gave the cis,cis-quatercyclopropane (S*,S*,R*,R*)-21 as the main product (58 % yield) along with the cis,trans-diastereomer (S*,S*,R*,S*)-18 (29 % yield). Thus, five of the six possible diastereomeric quatercyclopropanes were obtained from meso-5, d,l-5, and (Z)-cis-16. The X-ray crystal structure analyses of trans,trans-(R*,S*,R*,S*)-17 and cis,cis-(S*,S*,R*,R*)-21 revealed for the both an unusual conformation in which the central bicyclopropyl unit adopts an s-trans-(antiperiplanar) orientation with phi=180.0 degrees , and the two terminal bicyclopropyl moieties adopt a synclinal conformation with phi=49.8 and 72.0 degrees , respectively. In solution the vicinal coupling constants (3)J(H,H) in trans,trans-(R*,S*,R*,S*)-[D(14)]-17, trans,trans-(R*,S*,S*,R*)-[D(14)]-19, trans,cis-(R*,S*,R*,R*)-[D(14)]-18 and trans,cis-(R*,S*,S*,S*)-[D(14)]-20 were found to be 4.1, 4.7, 5.9 and 5.9 Hz, respectively. This indicates a predominance of the all-gauche conformer in (R*,S*,R*,S*)-17 and a decreasing fraction of it in this sequence of the other diastereomers.     

Expedient method for the transmetalation of Zn(II)-centered salphen complexes

Various mono- and bis-ZnII complexes derived from salphen ligands have been conveniently transmetalated with a number of transition metal (TM) acetates (M=Ni, Pd, Mn) in THF to afford their respective TM-salphen counterparts in excellent isolated yields (80-100%). This new transmetalation procedure allows in situ switching between supramolecular and catalytic functions of the metallosalphen complex.     

Quantitation of 17beta-nandrolone metabolites in boar and horse urine by gas chromatography-mass spectrometry

A method to quantify metabolites of 17beta-nandrolone (17betaN) in boar and horse urine has been optimized and validated. Metabolites excreted in free form were extracted at pH 9.5 with tert-butylmethylether. The aqueous phases were applied to Sep Pak C18 cartridges and conjugated steroids were eluted with methanol. After evaporation to dryness, either enzymatic hydrolysis with beta-glucuronidase from Escherichia coli or solvolysis with a mixture of ethylacetate:methanol:concentrated sulphuric acid were applied to the extract. Deconjugated steroids were then extracted at alkaline pH with tert-butylmethylether. The dried organic extracts were derivatized with MSTFA:NH4I:2-mercaptoethanol to obtain the TMS derivatives, and were subjected to analysis by gas chromatography mass spectrometry (GC/MS). The procedure was validated in boar and horse urine for the following metabolites: norandrosterone, noretiocholanolone, norepiandrosterone, 5beta-estran-3alpha, 17beta-diol, 5alpha-estran-3beta, 17beta-diol, 5alpha-estran-3beta, 17alpha-diol, 17alpha-nandrolone, 17betaN, 5(10)-estrene-3alpha, 17alpha-diol, 17alpha-estradiol and 17beta-estradiol in the different metabolic fractions. Extraction recoveries were higher than 90% for all analytes in the free fraction, and better than 80% in the glucuronide and sulphate fractions, except for 17alpha-estradiol in the glucuronide fraction (74%), and 5alpha-estran-3beta, 17alpha-diol and 17betaN in the sulphate fraction (close to 70%). Limits of quantitation ranged from 0.05 to 2.1 ng mL(-1) in the free fraction, from 0.3 to 1.7 ng mL(-1) in the glucuronide fraction, and from 0.2 to 2.6 ng mL(-1) in the sulphate fraction. Intra- and inter-assay values for precision, measured as relative standard deviation, and accuracy, measured as relative standard error, were below 15% for most of the analytes and below 25%, for the rest of analytes. The method was applied to the analysis of urine samples collected after administration of 17betaN laureate to boars and horses, and its suitability for the quantitation of the metabolites in the three fractions has been demonstrated.     

Preparation and structure of three solvatomorphs of the polymer [Co(dbm)2(4ptz)]n: spin canting depending on the supramolecular organization

The syntheses and X-ray structures of three isomeric 1D coordination polymers are reported. The complex [Co(dbm)2(MeOH)2] (1) was used as a precursor in these reactions. The preparation and structure of 1 is also presented; this mononuclear complex is in the cis configuration because this allows the formation of a network of intermolecular hydrogen bonds in the solid state. Reaction of 1 with 2,4,6-tris-(4-pyridyl)-1,3,5-triazine (4ptz) yields the polymers [Co(dbm)2(4ptz)]n.nTHF (2a), [Co(dbm)2(4ptz)]n.0.75nTHF.0.5nEt2O (2b), and [Co(dbm)2(4ptz)]n.3nDMF (2c) in the form of zigzag chains, instead of the expected honeycomb architectures. This is because of the establishment of extended pi-pi stacking throughout these solids, which could not have occurred otherwise. Compounds 2a, 2b, and 2c are solvatomorphs, and formation of either one of them depends on the exact conditions of crystallization, which lead to significant differences in the supramolecular organization of the chains. Bulk magnetic measurements on 2a reveal weak antiferromagnetic exchange within the chains and small ordering throughout the solid that results in the manifestation of the phenomenon of spin canting, whereas for 2c the different supramolecular organization causes the antiferromagnetic exchange not to result in spin canting.     

Combined theoretical and experimental analysis of the bonding in the heterobimetallic cubane-type Mo(3)NiS(4) and Mo(3)CuS(4) core clusters

X-ray structural data for the cubane-type clusters [Mo3CuS4(dmpe)3Cl4](+) and Mo3NiS4(dmpe)3Cl4 (dmpe = 1,2-bis(dimethylphosphino)ethane) with 16 metal electrons have been compared with optimized structural parameters calculated using "ab initio" methodologies. Compound Mo3NiS4(dmpe)3Cl4 crystallizes in the cubic noncentrosymmetric space group P213 with a Mo-Ni distance of 2.647 Angstrom, that is 0.2 Angstrom shorter than the Mo-Cu bond length in the isoelectronic copper cluster. The best agreement between theory and experiments has been obtained using the B3P86 method. In order to validate the B3P86 results, accurate infrared and Raman spectra have been acquired and the vibrational modes associated to the cubane-type Mo3M'S4 (M' = Cu or Ni) unit have been assigned theoretically. The electronic changes taking place when incorporating the M' into the Mo3S4 unit have been analyzed from a theoretical and experimental perspective. The bond dissociation energies between M'-Cl and Mo3S4 fragments show that formation of [Mo3CuS4(dmpe)3Cl4](+) is 135 kcal/mol energetically less favorable than the Ni incorporation. The more robust nature of the Mo3NiS4 fragment has been confirmed by mass spectrometry. The X-ray photoelectron spectroscopy (XPS) spectra of the trimetallic and tetrametallic complexes have been measured and the obtained binding energies compared with the computed electronic populations based on topological approaches of the electron localization function (ELF). The energies and shapes of the Cu 2p and Ni 2p lines indicate formal oxidation states of Cu(I) and Ni(II). However, the reductive addition of nickel into [Mo3S4(dmpe)3Cl3](+) causes a small decrease in the Mo 3d binding energies. This fact prevents an unambiguous assignment of an oxidation state in a conventional way, a circumstance that has been analyzed through the covariance of the electronic populations associated to the C(M') core and V(Mo3Ni) and V(S(2)') valence basins where Mo3NiS4 is a particularly electronically delocalized chemical entity.