Synthesis of 2′‐O‐[(Triisopropylsilyl)oxy]methyl (= tom)‐Protected Ribonucleoside Phosphoramidites Containing Various Nucleobase Analogues

The first results of a study aiming at an efficient preparation of a large variety of 2′‐O‐[(triisopropylsilyl)oxy]methyl(= tom)‐protected ribonucleoside phosphoramidite building blocks containing modified nucleobases are reported. All of the here presented nucleosides have already been incorporated into RNA sequences by several other groups, employing 2′‐O‐tbdms‐ or 2′‐O‐tom‐protected phosphoramidite building blocks (tbdms = (tert‐butyl)dimethylsilyl). We now optimized existing reactions, developed some new and shorter synthetic strategies, and sometimes introduced other nucleobase‐protecting groups. The 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides N²‐acetylisocytidine 5 , O²‐(diphenylcarbamoyl)‐N⁶‐isobutyrylisoguanosine 8 , N⁶‐isobutyryl‐N²‐(methoxyacetyl)purine‐2,6‐diamine ribonucleoside (= N⁸‐isobutyryl‐2‐[(methoxyacetyl)amino]adenosine) 11 , 5‐methyluridine 13 , and 5,6‐dihydrouridine 15 were prepared by first introducing the nucleobase protecting groups and the dimethoxytrityl group, respectively, followed by the 2′‐O‐tom group (Scheme 1). The other presented 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides inosine 17 , 1‐methylinosine 18 , N⁶‐isopent‐2‐enyladenosine 21 , N⁶‐methyladenosine 22 , N⁶,N⁶‐dimethyladenosine 23 , 1‐methylguanosine 25 , N²‐methylguanosine 27 , N²,N²‐dimethylguanosine 29 , N⁶‐(chloroacetyl)‐1‐methyladenosine 32 , N⁶‐{{{(1S,2R)‐2‐{[(tert‐butyl)dimethylsilyl]oxy}‐1‐{[2‐(4‐nitrophenyl)ethoxy]carbonyl}propyl}amino}carbonyl}}adenosine 34 (derived from L ‐threonine) and N⁴‐acetyl‐5‐methylcytidine 36 were prepared by nucleobase transformation reactions from standard, already 2′‐O‐tom‐protected ribonucleosides (Schemes 2–4). Finally, all these nucleosides were transformed into the corresponding phosphoramidites 37 – 52 (Scheme 5), which are fully compatible with the assembly and deprotection conditions for standard RNA synthesis based on 2′‐O‐tom‐protected monomeric building blocks.     

Synthesis of Selectively 15N‐Labeled 2′‐O‐{[(Triisopropylsilyl)oxy]methyl}(=tom)‐Protected Ribonucleoside Phosphoramidites and Their Incorporation into a Bistable 32Mer RNA Sequence

We present optimized reaction conditions for the conversion of 2′‐O‐{[(triisopropylsilyl)oxy]methyl}(=tom) protected uridine and adenosine nucleosides into the corresponding protected (3‐¹⁵N)‐labeled uridine and cytidine and (1‐¹⁵N)‐labeled adenosine and guanosine nucleosides 4, 6, 12 , and 18 , respectively (Schemes 1–4). On a DNA synthesizer, the resulting ¹⁵N‐labeled 2′‐O‐tom‐protected phosphoramidite building blocks 19 – 22 were efficiently incorporated into five selected positions of a bistable 32mer RNA sequence 23 (known to adopt two different structures) (Fig. 1). By 2D‐HSQC and HNN‐COSY experiments in H₂O/D₂O 9 : 1, the ¹⁵N‐signals of all base‐paired ¹⁵N‐labeled nucleotides could be identified and attributed to one of the two coexisting structures of 23 .     

Synthesis of (2′S)‐2′‐Deoxy‐2′‐C‐methylpurine Nucleosides and Their Phosphoramidites

We describe the stereoselective synthesis of (2′S)‐2′‐deoxy‐2′‐C‐methyladenosine ( 12 ) and (2′S)‐2′‐deoxy‐2′‐C‐methylinosine ( 14 ) as well as their corresponding cyanoethyl phosphoramidites 16 and 19 from 6‐O‐(2,6‐dichlorophenyl)inosine as starting material. The methyl group at the 2′‐position was introduced via a Wittig reaction (→ 3 , Scheme 1) followed by a stereoselective oxidation with OsO₄ (→ 4 , Scheme 2). The primary‐alcohol moiety of 4 was tosylated (→ 5 ) and regioselectively reduced with NaBH₄ (→ 6 ). Subsequent reduction of the 2′‐alcohol moiety with Bu₃SnH yielded stereoselectively the corresponding (2′S)‐2′‐deoxy‐2′‐C‐methylnucleoside (→ 8a ).     

Nucleotides,Part LXVIII,Acetals as New 2′‐O‐Protecting Functions for the Synthesis of Oligoribonucleotides: Synthesis of Monomeric Building Units and Oligoribonucleotides

For the efficient synthesis of oligoribonucleotides by the 5′‐O‐(4,4′‐dimethoxytrityl) phosphoramidite approach, the 2′‐O‐[1‐(benzyloxy)ethyl]acetals 56 – 67 were investigated. Studies with the 2′‐O‐[1‐(benzyloxy)ethyl]‐5′‐O‐(dimethoxytrityl)ribonucleoside 3′‐phosphoramidites 56 – 59 gave, however, only reasonable results. The oligoribonucleotides obtained showed some impurities since the acid stabilities of the acetal and dimethoxytrityl functions are too close to guarantee a high selectivity. A combination of new acid‐labile protected 2′‐O‐protecting groups with the 2‐(4‐nitrophenyl)ethyl/[2‐(4‐nitrophenyl)ethoxy]carbonyl (npe/npeoc) strategy for base protection was more successful. The synthesis and physical properties of the monomeric building units and their intermediates 8 – 67 and the conditions for the automated generation of homo‐ and mixed oligoribonucleotides is described. The new 2′‐acetal protecting group could be cleaved off in a two step procedure and was designed for levelling their stability with regard to the attached nucleobase as well. Therefore, we used the 1‐{{3‐fluoro‐4‐{{[2‐(4‐nitrophenyl)ethoxy]carbonyl}oxy}benzyl}oxy}ethyl (fnebe) moiety for the protection of 2′‐OH of uridine, and for that of 2′‐OH of A, C, and G, the 1‐{{4‐{{[2‐(4‐nitrophenyl)ethoxy]carbonyl}oxy}benzyl}oxy}ethyl (nebe) residue. After selective deprotection by β‐elimination induced by a strong organic base like DBU, the remaining activated acetal was hydrolyzed under very mild acidic protic conditions, which reduced 2′‐3′ isomerization and chain cleavage. Also storage, handling, and purification of the chemically and enzymatically sensitive oligomers was simplified by this approach.     

Synthesis and Incorporation of C(5′)‐Ethynylated Uracil‐Derived Phosphoramidites into RNA

The D ‐allo‐ and L ‐talo‐hept‐6‐ynofuranosyluracil‐derived phosphoramidites 11A and 11T were prepared in 9–10% yield over eight steps from the previously described propargylic alcohols 1A and 1T , respectively. The corresponding nucleotides were incorporated into rU₁₄ by standard solid‐phase synthesis. While the duplex consisting of rU₁₄ with one L ‐talo‐hept‐6‐ynofuranosyluracil in the middle of the strand and rA₁₄ ( I ? V ) had the same melting point as the reference duplex rU₁₄?rA₁₄ ( I ? II ), the duplex with one D ‐allo‐hept‐6‐ynofuranosyluracil in the middle of rU₁₄ and rA₁₄ ( I ? III ) melted 1.5° lower than the reference duplex. The duplex I ? VI consisting of rU₁₄ with six L ‐talo‐hept‐6‐ynofuranosyluracils distributed over the entire strand and rA₁₄ showed a melting point that is 11° lower than the reference duplex. The corresponding duplex I ? IV of rU₁₄ possessing six D ‐allo‐hept‐6‐ynofuranosyluracils and rA₁₄ showed a melting point which is more than 20° below the one of the reference duplex. These results are in qualitative agreement with the predictions based on the conformational analysis of the nucleosides and the interference of the ethynyl moiety with the hydration of the oligonucleotides.     

Polymorph of {2‐[(2‐hydroxyethyl)iminiomethyl]phenolato‐κO}dioxido{2‐[(2‐oxidoethyl)iminomethyl]phenolato‐κ3O,N,O′}molybdenum(VI)

A second polymorphic form (form I) of the previously reported compound {2‐[(2‐hydroxyethyl)iminiomethyl]phenolato‐κO}dioxido{2‐[(2‐oxidoethyl)iminomethyl]phenolato‐κ³O,N,O′}molybdenum(VI) (form II), [Mo(C₉H₉NO₂)O₂(C₉H₁₁NO₂)], is presented. The title structure differs from the previously reported polymorph [Głowiak, Jerzykiewicz, Sobczak & Ziółkowski (2003). Inorg. Chim. Acta, 356 , 387–392] by the fact that the asymmetric unit contains three molecules linked by O—H...O hydrogen bonds. These trimeric units are further linked through O—H...O hydrogen bonds to form a chain parallel to the [11] direction. As in the previous polymorph, each molecule is built up from an MoO₂²⁺ cation surrounded by an O,N,O′‐tridentate ligand (O⁻C₆H₄CH=NCH₂CH₂O⁻) and weakly coordinated by a second zwitterionic ligand (O⁻C₆H₄CH=N⁺HC₂H₄OH). All complexes are chiral with the absolute configuration at Mo being C or A. The main difference between the two polymorphs results from the alternation of the chirality at Mo within the chain.     

Molecular structures of 3‐[(2,2,3,3‐tetrafluoropropoxy)methyl]‐ and 3‐[(2,2,3,3,3‐pentafluoropropoxy)methyl]pyridinium saccharinates

The salts 3‐[(2,2,3,3‐tetrafluoropropoxy)methyl]pyridinium saccharinate, C₉H₁₀F₄NO⁺·C₇H₄NO₃S⁻, (1), and 3‐[(2,2,3,3,3‐pentafluoropropoxy)methyl]pyridinium saccharinate, C₉H₉F₅NO⁺·C₇H₄NO₃S⁻, (2), i.e. saccharinate (or 1,1‐dioxo‐1λ⁶,2‐benzothiazol‐3‐olate) salts of pyridinium with –CH₂OCH₂CF₂CF₂H and –CH₂OCH₂CF₂CF₃meta substituents, respectively, were investigated crystallographically in order to compare their fluorine‐related weak interactions in the solid state. Both salts demonstrate a stable synthon formed by the pyridinium cation and the saccharinate anion, in which a seven‐membered ring reveals a double hydrogen‐bonding pattern. The twist between the pyridinium plane and the saccharinate plane in (2) is 21.26 (8)° and that in (1) is 8.03 (6)°. Both salts also show stacks of alternating cation–anion π‐interactions. The layer distances, calculated from the centroid of the saccharinate plane to the neighbouring pyridinium planes, above and below, are 3.406 (2) and 3.517 (2) Å in (1), and 3.409 (3) and 3.458 (3) Å in (2).     

N‐[(Diphenoxyphosphoryl)oxy]‐2‐phenyl‐1H‐benzimidazole as a versatile reagent for synthesis O‐alkylhydroxamic acids

Highly efficient reagent, N‐[(diphenoxyphosphoryl)oxy]‐2‐phenyl‐1H‐benzimidazole was synthesized and its applicability was demonstrated for the synthesis of O‐alkyl hydroxamic acids. The efficiency of the reagent was evaluated through the synthesis of range of O‐alkyl hydroxamic acids from aromatic carboxylic acids as well as N‐protected amino acids. The enatiomeric purity of synthesized compounds was measured using chiral HPLC and the degree of racemization that occurred was found to be negligible.     

Benzyl N‐[(Benzyloxy)methyl]carbamate: An Improved Aminomethylation Electrophile for the Synthesis of (Benzyloxy)carbonyl (Cbz)‐Protected Chiral β2‐Amino Acids

α‐Aminomethylation of (R)‐DIOZ‐alkylated (DIOZ=4‐isopropyl‐5,5‐diphenyloxazolidin‐2‐one) substrates is a key step in the asymmetric synthesis of β²‐amino acids, but it is unfortunately often accompanied by formation of transcarbamation by‐products. Aminomethylation was tested using a range of electrophiles, and the amount of by‐product formation was assessed in each case. Benzyl N‐[(benzyloxy)methyl]carbamate electrophile 3d is unable to form this by‐product due to its inherent benzyl substitution. Use of electrophile 3d showed an improved impurity profile in aminomethylation, thus leading to easier intermediate purification.     

Poly[[[(1,2‐η)‐benzene]silver(I)]‐μ‐trifluoromethanesulfonate‐O;O′;O′′:O′′]

The title compound, [Ag(CF₃O₃S)(C₆H₆)], has been synthesized and characterized by low‐temperature single‐crystal X‐ray diffraction. The complex is polymeric, with a network of tri­fluoro­methane­sulfonate anions bridging the silver cations. The terminal planar benzene ligand is asymmetrically η²‐coordinated to the Ag.     

Bis(μ‐succinato‐O,O′:O′′,O′′′)bis[bis(2‐amino‐1,3‐benzothiazole‐N3)copper(II)]

In the title dimeric complex, [Cu₂(C₄H₄O₄)₂(C₇H₆N₂S)₄], which possesses a centre of symmetry, the Cu atoms are enclosed in a 14‐membered ring. They adopt a distorted square‐bipyramidal (4+2) coordination. The four closest donor atoms are two N atoms of 2‐amino­benzo­thiazole ligands and two O atoms of the succinate carboxylate groups. They form a square‐planar cis arrangement, with an average Cu—N distance of 2.003 (3) Å and Cu—O distances of 1.949 (3) and 1.965 (3) Å. Two longer Cu—O bonds of 2.709 (3) and 2.613 (3) Å involving the remaining O atoms of the carboxylate groups complete the sixfold coordination of the Cu atoms. The H atoms of each amino group of the 2‐amino­benzo­thiazole molecules form intra‐ and inter­molecular N—H?O hydrogen bonds. A nearly perpendicular inter­molecular C—H?Cg interaction (Cg is the centroid of the imidazole ring) is observed. The intramolecular Cu?Cu distance is 6.384 (2) Å.     

Synthesis of Photolabile 5′‐O‐Phosphoramidites for the Photolithographic Production of Microarrays of Inversely Oriented Oligonucleotides

The photolabile 3′‐O‐{[2‐(2‐nitrophenyl)propoxy]carbonyl}‐protected 5′‐phosphoramidites ( 16 – 18 ) were synthesized (see Scheme) for an alternative mode of light‐directed production of oligonucleotide arrays. Because of the characteristics of these monomeric building blocks, photolithographic in situ DNA synthesis occurred in 5′→3′ direction, in agreement with the orientation of enzymatic synthesis. Synthesis yields were as good as those of conventional reactions. The resulting oligonucleotides are attached to the surface via their 5′‐termini, while the 3′‐hydroxy groups are available as substrates for enzymatic reactions such as primer extension upon hybridization of a DNA template (see Fig. 2). The production of such oligonucleotide chips adds new procedural avenues to the growing number of applications of DNA microarrays.     

Synthesis and characterization of near‐monodisperse electron acceptor homopolymers of 2‐[(3,5‐dinitrobenzoyl)oxy]ethyl methacrylate

Homopolymers of 2‐(trimethylsiloxy)ethyl methacrylate of degrees of polymerization from 5 to 50 were synthesized by group transfer polymerization in tetrahydrofuran (THF) using 1‐methoxy‐1‐(trimethylsiloxy)‐2‐methyl propene as the initiator and tetrabutylammonium bibenzoate as the catalyst. These polymers were first converted to poly[2‐(hydroxy)ethyl methacrylate]s by removal of the trimethylsilyl‐protecting groups by acidic hydrolysis, and subsequently transformed to poly{2‐[(3,5‐dinitrobenzoyl)oxy]ethyl methacrylate}s by reaction with 3,5‐dinitrobenzoyl chloride in the presence of triethylamine. Gel permeation chromatography in THF and proton nuclear magnetic resonance (¹H NMR) spectroscopy in CDCl₃ and d₆ dimethyl sulfoxide were used to characterize the polymers in terms of their molecular weight and composition. The molecular weights were found to be close to the values expected from the polymerization stoichiometry and the molecular weight distributions were narrow, with polydispersity indices around 1.1. The hydrolysis and reesterification steps were found to be almost quantitative for all polymers. Differential scanning calorimetry and thermal gravimetric analysis were also employed to measure the glass transition temperatures (T_g 's) and decomposition temperatures, which were determined to be approximately 80 and 320 °C, respectively. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1457–1465, 2000     

3‐[(Diphenylphosphinothioyl)oxy]‐N‐methylpropan‐1‐aminium diphenylphosphanylthioate

The title salt, C₁₆H₂₁NOPS⁺·C₁₂H₁₀OPS, was synthesized from the reaction between 3‐(methylamino)propan‐1‐ol and PPh₂(S)Cl in the presence of Et₃N. Its structure has been identified using spectroscopic methods and X‐ray analysis. Single crystals were obtained from ethanol by slow evaporation. In the asymmetric unit, a cation–anion pair is formed through an intermolecular N—H...O [N...O = 2.6974 (18) Å] hydrogen bond. The molecules are packed through N—H...O and N—H...S hydrogen bonds in the crystal and these hydrogen bonds are responsible for the high melting point. The P atoms of the anion and cation both have distorted tetrahedral environments.     

Bis(2,6‐diamino‐1H‐purin‐3‐ium) di‐μ‐croconato‐κ3O,O′:O′′;κ3O:O′,O′′‐bis[tetraaqua(croconato‐κ2O,O′)neodymium(III)]

The structure of the ionic title compound, (C₅H₇N₆)₂[Nd₂(C₅O₅)₄(H₂O)₈], consists of anionic dimers built around an inversion centre and is made up of an Nd^III cation, two croconate (croco) dianions and four water molecules (plus their inversion images), with two noncoordinated symmetry‐related 2,6‐diamino‐1H‐purin‐3‐ium (Hdap⁺) cations providing charge balance. Each Nd^III atom is bound to nine O atoms from four water and three croco units. The coordination polyhedron has the form of a rather regular monocapped square antiprism. The croconate anions are regular and the Hdap⁺ cation presents a unique, thus far unreported, protonation state. The abundance of hydrogen‐bonding donors and acceptors gives rise to a complex packing scheme consisting of dimers interlinked along the three crystallographic directions and defining anionic `cages' where the unbound Hdap⁺ cations lodge, linking to the mainframe via (N—H)_Hdap...O_water/croco and (O—H)_water...N_Hdap interactions.     

Synthesis of 1‐[(pyrazol‐3‐yl)methyl]pyridazin‐6‐ones

This paper presents the synthesis of 1‐[(pyrazol‐3‐yl)methyl]pyridazin‐6‐ones from ethyl 4‐(4,5‐dichloro‐6‐oxopyridazin‐1‐yl)‐3‐oxobutanoate.     

Poly­[manganese(II)‐μ2‐benzidine‐κ2N:N′‐μ3‐bi­phenyl‐2,2′‐di­carboxylato‐κ4O:O′,O′′:O′′′]

The title compound, [Mn(C₁₄H₈O₄)(C₁₂H₁₂N₂)]_n, with a novel three‐dimensional framework, has been prepared by a hydro­thermal reaction at 433 K. Each Mn atom lies on a twofold axis in a slightly distorted octahedral geometry, coordinated by two N atoms from two benzidine ligands and four O atoms from three symmetry‐related biphenyl‐2,2′‐dicarboxylate (bpdc) ligands. The benzidine ligands lie about inversion centres and the bpdc ligands about twofold axes. Each bpdc ligand is bonded to three Mn ions to form a continuous chain of metal ions. The bpdc ligands are accommodated in a series of distorted holes resembling hexagonal prisms.     

Poly­[[[(1,10‐phenanthroline‐κ2N,N′)­zinc(II)]‐μ3‐5‐hydroxy­isophthalato‐κ4O,O′:O′′:O′′′] monohydrate]

In the title compound, {[Zn(C₈H₄O₅)(C₁₂H₈N₂)]·H₂O}_n or {[Zn(OH‐BDC)(phen)]·H₂O}_n (where OH‐H₂BDC is 5‐hydroxy­isophthalic acid and phen is 1,10‐phenanthroline), the Zn atoms are coordinated by two N atoms from the phen ligands and by four O atoms from hydroxy­isophthalate ligands in a highly distorted octahedral geometry, with Zn—O distances in the range 2.042 (4)–2.085 (5) Å and Zn—N distances of 2.133 (5) and 2.137 (5) Å. The {[Zn(OH‐BDC)(phen)]·H₂O}_n infinite zigzag polymer forms a helical chain of [Zn₂(OH‐BDC)₂]_n units. Face‐to‐face π–π interactions (3.60–3.75 Å) occur between two phen rings belonging to the same helical chain. Consolidation of the packing structure is achieved by O—H⋯O hydrogen‐bonding interactions between the carboxyl­ate O atoms, the hydroxyl group and the water mol­ecule, forming two‐dimensional sheets.