On the Karplus relation for 3J(POCC) of nucleotides

The original Karplus parameters for analysing ³J(POCC) magnitudes of nucleotides in terms of conformational properties of the O? C bond were taken from results for 3′,5′-nucleotides and applied to 3′→ 5′-oligonucleotides; the parameters were later modified to take account of ‘largey’ magnitudes of ³J(POCC) observed in 2′ → 5′-oligonucleotides. In this work the origin of this discrepancy is explained in terms of substituent electronegativity effects at C-1′, and quantified using the ¹³C NMR results of 2′,3′-cyclic mononucleotides. A new set of Karplus parameters suitable for analysing ³J(POCC) magnitudes in 3′- and 5′-nucleotides and 3′ → 5′-oligonucleotides is determined from ¹³C NMR measurements on 3′-nucleotides and available results for 3′,5′-cyclic mononucleotides. A method of dealing with J(P, C-1′) coupling in 2′-nucleotides, 2′,3′-cyclic nucleotides and 2′ → 5′-oligonucleotides using the same Karplus relationship is suggested.     

Kinetic Study of the Ru(II) Catalyzed Oxidation of Pentacyanoferrate(ll) Complexes by Peroxydisulfate

The oxidation reactions of Fe(CN)₅L^3? (L = 4-ampy, py, dpa) complexes by S₂O₈^2? were catalyzed upon the addition of a trace amount of Ru(NH₃)₅L′²⁺ (L′ = pz, py or dcb) complex, and the reaction becomes zero-order in Fe(II). The reaction time is ～10² fold faster than the simple Fe(CN)₅L^3?-S₂O₈^2? system. The mechanism of this Ru(II) catalyzed redox reaction is proposed as Ru(NH₃)₅L′²⁺ + 1/2 S₂O₈^2? → Ru(NH₃)₅L′³⁺ + SO₄^2? Ru(NH₃)₅L′³⁺ + Fe(CN)₅L^3? ? Ru(NH₃)₅L′²⁺ + Fe(CN)₅L^2?     

Reisolation of Carotenoid 3,6-Epoxides from Red Paprika (Capsicum annuum)

Cucurbitaxanthin A (= (3S,5R,6R,3′R)-3,6-epoxy-5,6-dihydro-β,β- carotene-5,3′-diol; 5 ), cucurbitaxanthin B (= (3S,5R,6R,3′S,5′R,6′S)-3,6,5′, 6′-diepoxy-5,6,5′,6′-tetrahydro-β,β-carotene-5,3′-diol; 6 ), the epimeric cucurbitachromes 1 and 2 (= (3S,5R,6R,3′S,5′R,8′S)- and (3S,5R,6R,3′S,5′R,8′R)-3,6,5′, 8′-diepoxy-5,6,5′,6′-tetrahydro-β,β-carotene-5,3′-diol, resp.; 9/10 ), cycloviolaxanthin (= (3S,5R,6R,3′S,5′R,6′R)-3,6,3′, 6′-diepoxy-5,6,5′,6′-tetrahydro-β,κs-carotene-5,5′-diol; 8 ), and capsanthin 3,6-epoxide (= (3S,5R,6R,3′S,5′R)-3,6-epoxy-5,6-dihydro ?5,3′-dihydroxy-β,κ-caroten-6′-one; 7 ) were isolated from red spice paprika (Capsicum annuum var. longum) and characterized by their ¹H- and ¹³C-NMR, mass, and CD spectra.     

Preparation and (E/Z)‐Isomerization of the Diastereoisomers of Violaxanthin

Violaxanthin A (=(all‐E,3S,5S,6R,3′S,5′S,6′R)‐5,6 : 5′,6′‐diepoxy‐5,6,5′,6′‐tetrahydro‐β,β‐carotene‐3,3′‐diol =syn,syn‐violaxanthin; 5 ) and violaxanthin B (=(all‐E,3S,5S,6R,3′S,5′R,6′S)‐5,6 : 5′,6′‐diepoxy‐5,6,5′,6′‐tetrahydro‐β,β‐carotene‐3,3′‐diol=syn,anti‐violaxanthin; 6 ) were prepared by epoxidation of zeaxanthin diacetate ( 1 ) with monoperphthalic acid. Violaxanthins 5 and 6 were submitted to thermal isomerization and I₂‐catalyzed photoisomerization. The structure of the main products, i.e., (9Z)‐ 5 , (13Z)‐ 5 , (9Z)‐ 6 , (9′Z)‐ 6 , (13Z)‐ 6 , and (13′Z)‐ 6 , was determined by their UV/VIS, CD, ¹H‐NMR, ¹³C‐NMR, and mass spectra.     

Semiempirical studies on the interactions of dialkyldi(aquo)tin cations, [R2Sn(H2O)2]2+, with selected nucleotides

Semiempirical calculations have been carried out on the interactions of [R₂Sn(H₂O)₂]²⁺, [R = H(CH₂)_n: n = 1–8], mainly with five nucleotides, 5′‐adenosine monophosphate (5′‐AMP), but also with guanosine 5′‐monophosphate (5′‐GMP), cytidine 5′‐monophosphate (5′‐CMP), uridine‐5′‐monophosphate (5′‐UMP) and inosine 5′‐monophosphate (5′‐IMP). The preferred sites of interaction were calculated to be the ribose O2 and O3 hydroxyl oxygens and/or the phosphate oxygens, with the nitrogen sites in the bases the least attractive to the tin compounds. This is in general agreement with experimental findings. Structures of the 1:1 coordination complexes vary from distorted tetrahedral, to distorted trigonal pyramidal to distorted octahedral geometries. Copyright © 2007 John Wiley & Sons, Ltd.     

Diorgano-tellur-bis-(dialkylcarbamate) und -(dithiocarbamate)

Diorganyltellurium Bis-(dialkylcarbamates) and -(dithiocarbamates) Compounds of the type R₂Te(X₂CNR′₂)₂, with R ? C₆H₅, CH₃; R′ ? CH₃, C₂H₅, i-C₃H₇, c-C₆H₁₁, C₆H₅, and X ? S, are obtained by reaction of dimethyltellurium with tetraorganyl-thiuram-disulfides. Dimethyltellurium diiodide or diphenyltellurium dichloride react with sodium dithiocarbamates or with in situ prepared ammonium dithiocarbamates. Some compounds can be synthesized by reaction of diphenyltellurium oxide with amine in solutions of carbon disulfide. The synthesis of diphenyltellurium- and dimethyltellurium bis-(dimethylcarbamates) results from the interaction of diorganyltellurium diethanolate with dimethylammonium dimethylcarbamate. Decomposition reactions of the compounds in solid and solution are studied ¹H-NMR, ¹³C-NMR, and mass spectroscopically. Diorganyltellurium diethylen-bis-(N,N′-dimethyldithiocarbamates) are obtained by reaction of dimethyltellurium diiodide or diphenyltellurium dichloride and sodium ethylen-bis-(N,N′-dimethyldithiocarbamate) as polymeric products.     

Nucleotides,Part LXIII,New 2-(4-Nitrophenyl)ethyl(Npe)- and 2-(4-Nitrophenyl)ethoxycarbonyl(Npeoc)-Protected 2′-Deoxyribonucleosides and Their 3′-Phosphoramidites – Versatile Building Blocks for Oligonucleotide Synthesis

A series of new base-protected and 5′-O-(4-monomethoxytrityl)- or 5′-O-(4,4′-dimethoxytrityl)-substituted 3′-(2-cyanoethyl diisopropylphosphoramidites) and 3′-[2-(4-nitrophenyl)ethyl diisopropylphosphoramidites] 52 – 66 and 67 – 82 , respectively, are prepared as potential building blocks for oligonucleotide synthesis (see Scheme). Thus, 3′,5′-di-O-acyl- and N ²,3′-O,5′-O-triacyl-2′-deoxyguanosines can easily be converted into the corresponding O⁶-alkyl derivatives 6 , 8 , 10 , 12 , 14 , and 16 by a Mitsunobu reaction using the appropriate alcohol. Mild hydrolysis removes the acyl groups from the sugar moiety (→ 9 , 11 , 13 , 15 , and 19 (via 18 ), resp.) which can then be tritylated (→ 38 – 42 ) and phosphitylated (→ 57 – 61 ) in the usual manner. N ²-[2-(4-nitrophenyl)ethoxycarbonyl]-substituted and N ²-[2-(4-nitrophenyl)ethoxycarbonyl]-O⁶-[2-(4-nitrophenyl)ethyl]-substituted 2′-deoxyguanosines 5 and 7 , respectively, are synthesized as new starting materials for tritylation (→ 28 , 35 , and 37 ) and phosphitylation (→ 54 , 56 , 70 , and 78 ). Various O⁴-alkylthymidines (see 20 – 24 ) are also converted to their 5′-O-dimethoxytrityl derivatives (see 43 – 47) and the corresponding phosphoramidites (see 62 – 66 and 79 – 82 ).     

Oxidative cleavage of the FeFe bond in [C5Me5Fe(CO)2]2 using ferrocinium ion: A facile route to the synthetically useful complexes [C5Me5Fe(CO)2(solvent)]+

Complexes of the type {Fp′(solvent)}⁺ PF₆^?, 3a–3d, (Fp′ = (η -C₅Me₅)Fe(CO)₂, solvent = THF, CH₃COCH₃, CH₃CN, or pyridine) are conveniently prepared by the reaction between Fp′₂ and Cp₂Fe⁺ PF₆ (Cp = η⁵-C₅H₅) in the solvent under ambient conditions. The complexes {Fp′L}⁺ PF₆^?, 3e–3g, (L = CO, PPh₃, P(OPh)₃) are readily prepared from {Fp′THF}⁺. Fp′H is formed by treatment of 3a with NaBH₄. Fp′SC(S)NMe₂ can be prepared from 3a or 3e and NaSC(S)NMe₂.     

Nucleosides. Part LI The 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) and 2-(2,4-dinitrophenyl)ethoxycarbonyl (dnpeoc) groups for protection of hydroxy functions in ribonucleosides and 2′ -deoxyribonucleosides

The Common 2′ -deoxypyrimidine and -purine nucleosides, thymidine ( 4 ), O⁴-[2-(4-nitrophenyl)ethyl]-thymidine ( 17 ), 2′-deoxy-N⁴-[2-(4-nitrophenyl)ethoxycarbonyl]cytidine ( 26 ), 2′-deoxy-N⁶-[2-(4-nitrophenyl)-ethoxycarbonyl]adenosine- 39 , and 2′-deoxy-N²-[2-(4-nitrophenyl)(ethoxycarbonyl]-O⁶-[2–4-nitrophenyl)ethyl]-guanosine ( 52 ) were further protected by the 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) and the 2-(2,4-dinitrophenyl)ethoxycarbonyl (dnpeoc) group at the OH functions of the sugar moiety to form new partially and fully blocked intermediates for nucleoside and nucleotide syntheses. The corresponding 5′-O-monomethoxytrityl derivatives 5 , 18 , 30 , 40 , and 56 were also used as starting material to synthesize some other intermediates which were not obtained by direct acylations. In the ribonucleoside series, the 5′ -O-monomethoxytrityl derivatives 14 , 36 , 49 , and 63 reacted with 2-(4-nitrophenyl) ethyl chloroformate ( 1 ) to the corresponding 2′,3′-bis-carbonates 15 , 37 , 50 , and 64 which were either detriylated to 16 , 38 , 51 , and 65 , respectively, or converted by 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) treatment to the 2′,3′-cyclic carbonates 66 – 69 . The newly synthesized compounds were characterized by elemental analyses and UV and ¹H-NMR spectra.     

Coordination Adducts of Niobium(V) and Tantalum(V) Azide M(N3)5 (M=Nb,Ta) with Nitrogen Donor Ligands and their Self‐Ionization

Several new donor–acceptor adducts of niobium and tantalum pentaazide with N‐donor ligands have been prepared from the pentafluorides by fluoride–azide exchange with Me₃SiN₃ in the presence of the corresponding donor ligand. With 2,2′‐bipyridine and 1,10‐phenanthroline, the self‐ionization products [MF₄(2,2′‐bipy)₂]⁺[M(N₃)₆]⁻, [M(N₃)₄(2,2′‐bipy)₂]⁺[M(N₃)₆]⁻ and [M(N₃)₄(1,10‐phen)₂]⁺[M(N₃)₆]⁻ were obtained. With the donor ligands 3,3′‐bipyridine and 4,4′‐bipyridine the neutral pentaazide adducts (M(N₃)₅)₂⋅L (M=Nb, Ta; L=3,3′‐bipy, 4,4′‐bipy) were formed.     

Influence of Chelating Groups on the Luminescence Properties of Europium(III) and Terbium(III) chelates in the 2,2′-bipyridine series

Eight different 2,2′-bipyridine derivatives, i.e. 2, 5, 8, 10, 12, 13, 15 , and 19 (Schemes 1 and 2), were prepared to study the influence of the chelating groups on the luminescence properties of their Eu^III and Tb^III chelates. According to our luminescence results, 2,2′-(methylenenitrilo)bis(acetic acid) as well as (methylenenitrilo)bis-(methylphosphonic acid) in 6- and 6′-position of 2,2′-bipyridine is a suitable group when developing luminescent markers for bioaffinity assays based on time-resolved luminescence measurement.     

Coordination Adducts of Niobium(V) and Tantalum(V) Azide M(N3)5 (M=Nb,Ta) with Nitrogen Donor Ligands and their Self‐Ionization

Several new donor–acceptor adducts of niobium and tantalum pentaazide with N‐donor ligands have been prepared from the pentafluorides by fluoride–azide exchange with Me₃SiN₃ in the presence of the corresponding donor ligand. With 2,2′‐bipyridine and 1,10‐phenanthroline, the self‐ionization products [MF₄(2,2′‐bipy)₂]⁺[M(N₃)₆]^?, [M(N₃)₄(2,2′‐bipy)₂]⁺[M(N₃)₆]^? and [M(N₃)₄(1,10‐phen)₂]⁺[M(N₃)₆]^? were obtained. With the donor ligands 3,3′‐bipyridine and 4,4′‐bipyridine the neutral pentaazide adducts (M(N₃)₅)₂?L (M=Nb, Ta; L=3,3′‐bipy, 4,4′‐bipy) were formed.     

Synthesis of 1-(3′-deoxy-β-D-glycero-pentofuran-2′-ulosyl)uracil by selective elimination reactions

For the synthesis of y 1-(3′-deoxy-β-D-glycero-pentofuran-2′-ulosyl)uracil (16), the precursor, 5′-O-benzoyl derivative (2),² was elaborated in a variety of ways. 1-(5′-O-Benzoyl-3′-O-tosyl-β-D- lyxofuranosyl)uracil (4)² was benzoylated to N³-benzoyl-1-(2′,5′-di-O-benzoyl-3′-O-tosyl-β-D- lyxofuranosyl)uracil (5), which directly yielded 2 on treatment with sodium benzoate. 1-(3′,5′-Di-O- benzoyl-2′-O-tosyl-β-D-lyxofuranosyl)uracil (8) and its 3′,5′-O-isopropylidene analog (10) resisted elimination reactions, thus proving absolute selectivity in the elimination of the derivatives of 1-β-D- lyxofuranosyl-uracil. Seeking a more economical path to 2, 1-(5′-O-benzoyl-β-D-lyxofuranosyl)uracil (11) was first benzoylated to give 2′,5′-di-O-benzoate (12), accompanied by 3′,5′-di- and 2′,3′,5′-tri-O- benzoate. Mesylation of the major product (12) gave 1-(2′,5′-di-O-benzoyl-3′-O-mesyl-β-D- lyxofuranosyl)uracil (15), which, on treatment with sodium benzoate, gave 2 in an highly improved yield. Basic hydrolysis on 2 gave compound 16.     

Isolation of dithiocarbamate anions as salts of biscyclopentadienyl titanium(IV) chelates

A series of [Cp₂TiL]⁺[RR′NCS₂]^? complexes, where L is the conjugate base of acetylacetone, benzoylacetone or 8-hydroxyquinoline and R = CH₃, R′ = C₆H₅CH₂; R = C₂H₅, R′ = C₆H₄CH₃; R = H, R′ = C₅H₉; RR′ = C₆H₁₂, have been synthesised in aqueous medium by the reaction of [Cp₂TiL]⁺Cl^? with RR′NCS^?₂Na⁺. Conductivity measurements in nitrobenzene solution indicate that these complexes are electrolytes. Both the IR and NMR studies demonstrate that the ligand L is chelating in all these complexes. Consequently, tetrahedral coordination about the titanium atom is proposed. In addition to these studies, elemental analyses and magnetic susceptibility have been carried out for these complexes.     

Alkaloids of the flora of Siberia and Altai: XX. Synthesis of 5-aryl(hetaryl)-substituted anthranilic acid esters

Cross-coupling of methyl 2-acetylamino-5-bromobenzoate and 5′-bromolappaconitine with aryl-, furyl-, pyridyl-, and 5-acetylthiophen-2-ylboronic acids or 1-(2-fluoroquinolin-3-yl)-4,4,5,5-tetramethyl-1,3,2-dioxaborolane gave the corresponding 5-aryl(hetaryl)-substituted anthranilic acid derivatives. The use of the two-phase toluene-water system as reaction medium and addition of tetrabutylammonium bromide allows the cross-coupling to be accomplished under mild conditions. The catalytic system Pd(dba)₂-AsPh₃ was found to be efficient in the cross-coupling of methyl 2-acetylamino-5-bromobenzoate with furyl- and pyridylboronic acids, whereas the system Pd(OAc)₂-(o-Tol)₃P ensured good results in the reactions of 5′-bromolappaconitine with hetarylboronic acids. Facile esterification at the C⁸-OH and C⁹-OH groups of the aconitane skeleton was observed in the reactions of 5′-bromolappaconitine and 5′-phenyllappaconitine with phenylboronic acid. 5′-Bromo-8,9-O-(phenylboranediyl)lappaconitine under the Suzuki reaction conditions underwent hydrolysis of the boronic ester moiety with formation of the cross-coupling product of 5′-bromolappaconitine with phenylboronic acid.     

Synthesis of nonanucleotide (14-20) of the dihydrouridine (D) loop of yeast alanine transfer RNA

This paper deals with the synthesis of nonanucleotide AGDCGGDAG_p of the dihydrouridine (D) loop of yeast alanine transfer RNA by ligation of chemically or enzymatically synthesized AGDCGG with excessive *pDAG_p in the presence of T₄-RNA ligase and the choice of the optimum conditions of 5′-phosphorylation and ligation of the fragments AG, AGDC, GG, GG_p and DAG which were the constituents of the named nonanucleotide. The final product, nonanucleoside octaphosphate, was obtained by removing 3′-terminal phosphate group of the nonanucleotide with polynucleotide kinase possessing 3′-phosphatase activity and was checked by the sequence analysis in accordance with AGDCGGDAG. It was found that the yield of 5′-phosphorylation of DMP or DAG were almost quantitative at 5-10°C. The synthetic AGDCGGDAG_p had been used for the total synthesis of t-RNA_y^A|a.     

Single‐Stranded DNA: Replacement of Canonical by Base‐Modified Nucleosides in the Minihairpin 5′‐d(GCGAAGC)‐3′ and Constructs with the Aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′

The minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) was modified either in the loop region, in the base‐paired stem, or at the 5′‐terminus by incorporation of base‐modified nucleosides. The thermal melting was correlated to the structural changes induced by the various donor‐acceptor properties of the nucleosides. Overhanging nonpaired nucleosides at the 5′‐terminus stabilized the hairpin, while a reverse of the dG³?dA⁵ sheared base pair to dA³?dG⁵ severely affected the stability. The combination of the minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) and the thrombin‐binding aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′ ( 2 (= 46 )) resulted in the new construct 5′‐d(GGTTGGGCGAAGC GGTTGG)‐3′ ( 43 ) arising by replacement of the 5′‐d(TGT)‐3′ loop of 2 by the minihairpin. The fused oligonucleotide 43 exhibits a two‐phase thermal transition indicating the presence of the two unaltered moieties. According to slight changes of the T_m values of the construct 43 as compared to the separate units 1 and 2 , cooperative distorsions are discussed.     

Complex formation reactions of two sterically hindered platinum(II) complexes with some N-bonding ligands

The kinetics of the complex formation reactions of two [(TL ^tBu)PtCl]⁺ and [Pt(tpdm)Cl]⁺ complexes (TL ^tBu = 2,6-bis[(1,3-di-tert-butylimidazolin-2-imino)methyl]pyridine and tpdm = terpyridinedimethane) with N-donor ligands, l-histidine (L-His), inosine (Ino), inosine-5′-monophosphate (5′-IMP) and guanosine-5′-monophosphate (5′-GMP), were studied. All reactions were studied under pseudo-first-order conditions as a function of nucleophile concentration and temperature in aqueous 0.1 M NaClO₄ solution in the presence of 10 mM NaCl using variable-temperature Uv–Vis spectrophotometry. The order of reactivity of the studied ligands is L-His > Ino > 5′-GMP > 5′-IMP. This order of reactivity is in relation to their electronic properties and structures. The mechanism of the substitution reactions is associative in nature as supported by the negative entropy of activation.     

Syntheses,structures of Mn(II), Ni(II), Cu(II) and Zn(II) coordination complexes based on 3,4,5-trifluorobenzeneseleninic acid and N-donor ligands

Abstract

Five new coordination complexes [Mn^II (L₁)₂(4,4′-bpy)]_n (1), [Ni^II (L₁)₂(4,4′-bpy)]_n (2), [Zn^II (L₁)₂(4,4′-bpy)]_n (3), [Cu^II (L₁)₂(phen)₂]Cl₂ (4) and [Cu^II ₂(L₁)₂(2,2′-bpy)₂]Cl₂ (5) (HL₁?=?3,4,5-trifluorobenzeneseleninic acid, 4,4′-bpy = 4,4′-bipyridine, 2,2′-bpy = 2,2′-bipyridine and phen = 1,10-phenanthroline), have been synthesized and characterized by single-crystal X-ray diffraction, powder X-ray diffraction (PXRD), elemental analysis and IR spectroscopy. Complexes 1–3 display similar layers structures. In 1–3, the adjacent layers are further connected through π···π interactions to form three-dimensional supramolecular structures. Complexes 4 and 5 show a dimer containing an eight-membered ring. The dimer extends into three-dimensional supramolecular structures through π···π interactions, C–H···F and C–H···Cl interactions.     

A convenient synthesis of s-(5′-deoxy-5′-adenosyl)- (±) -2-methylhomocysteine

The synthesis of $\text{S}$-(5′-deoxy-5′-adenosyl)-+-2-methylhomocysteine in two steps from ^+--2-methylmethionine is described.