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.     

Reliable Chemical Synthesis of Oligoribonucleotides (RNA) with 2′‐O‐[(Triisopropylsilyl)oxy]methyl(2′‐O‐tom)‐Protected Phosphoramidites

A method for the introduction of the 2′‐O‐[(triisopropylsilyl)oxy]methyl (=tom) group into N‐acetylated, 5′‐O‐dimethoxytritylated ribonucleosides is presented. The corresponding 2′‐O‐tom‐protected phosphoramidite building blocks were obtained in pure form and were successfully employed for the routine synthesis of oligoribonucleotides on DNA synthesizers. Under DNA coupling conditions (2.5 min coupling time for a 1.5‐μmol synthesis scale) and with 5‐(benzylthio)‐1H‐tetrazole (BTT) as activator, 2′‐O‐tom‐protected phosphoramidites exhibited average coupling yields >99.4%. The combination of N‐acetyl and 2′‐O‐tom protecting groups allowed a reliable and complete two‐step deprotection, first with MeNH₂ in EtOH/H₂O and then with Bu₄NF in THF, without concomitant destruction of the product RNA sequences.     

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.     

Di‐μ‐acetato‐O:O′‐di‐μ‐acetato‐O,O′:O′‐bis­{[(cyclo­penta­dienyl)tris­(di­methyl­phosphito‐P)­cobalt‐O,O′,O′′]neodymium(III)}

In the title compound, [{η⁵‐CpCo[P(O)(OMe)₂]₃}Nd(O₂CCH₃)₂]₂, with a centrosymmetric mol­ecule, each Nd atom has an eight‐coordination environment, surrounded by a tripodal {L_OMe = CpCo[P(O)(OMe)₂]₃} and four bridging acetato ligands. The coordination geometry around each Nd centre is described as a distorted square‐antiprism and the two different types of acetato ligands have μ‐O:O′‐ and μ‐O,O′:O′‐acetato coordination modes. The Nd—O distances are in the range 2.378 (4)–2.594 (5) Å and the Nd?Nd distance is 3.9913 (6) Å.     

Chlorido[N,N′‐dibenzyl‐N′′‐(trichloroacetyl)phosphoramidato‐κ2O,O′](1,10‐phenanthroline‐κ2N,N′)copper(II)

In the title complex, [Cu(C₁₆H₁₆Cl₃N₃O₂P)Cl(C₁₂H₈N₂)], the Cu^II cation presents a square‐pyramidal environment, where the CuO₂N₂ base is formed by two O atoms from carbonyl and phosphoryl groups, and by two N atoms from a 1,10‐phenanthroline molecule. A coordinated Cl atom occupies the apex. N—H...Cl hydrogen bonds link the molecules into one‐dimensional chains. The trichloromethyl group is rotationally disordered over two positions, with occupancies of 0.747 (7) and 0.253 (7).     

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 ).     

(12‐Hydro­xy­methyl‐5,5,7,12,14‐penta­methyl‐1,4,8,11‐tetra­aza­cyclo­tetra­decane‐N‐acetato‐N,N′,N′′,N′′′,O,O′)cobalt(III) chloride perchlorate monohydrate

In the title compound, [Co(C₁₈H₃₇N₄O₃)](ClO₄)Cl·H₂O, the Co^III ion has a distorted octahedral geometry, with four N atoms and two O atoms constituting the coordination sphere. The crystal structure is stabilized by a three‐dimensional network of hydrogen bonds.     

Oligonucleotide Analogues with a Nucleobase‐Including Backbone,Part 5, 2′‐Deoxy‐8‐(hydroxymethyl)adenosine‐ and 2′‐Deoxy‐6‐(hydroxymethyl)uridine‐Derived Phosphoramidites: Synthesis and Incorporation into 14‐Mer DNA Strands

The pairing propensity of new DNA analogues with a phosphinato group between O−C(3′) and a newly introduced OCH₂ group at C(8) and C(6) of 2′‐deoxyadenosine and 2′‐deoxyuridine, respectively, was evaluated by force‐field calculations and Maruzen model studies. These studies suggest that these analogues may form autonomous pairing systems, and that the incorporation of single modified units into DNA 14mers is compatible with duplex formation. To evaluate the incorporation, we prepared the required phosphoramidites 3 and 4 from 2′‐deoxyadenosine and 2′‐deoxyuridine, respectively. The phosphoramidite 5 was similarly prepared to estimate the influence of a CH₂OH group at C(8) on the duplex stability. The modified 14‐mers 6 – 9 were prepared by solid‐phase synthesis. Pairing studies show a decrease of the melting temperature by 2.5° for the duplex 13 ⋅ 9 , and of 6 – 8° for the duplexes 10 ⋅ 6 , 11 ⋅ 6 , 13 ⋅ 7 , and 14 ⋅ 8 , as compared to the unmodified duplexes.     

Aqua­(2,2′‐diamino‐4,4′‐bi‐1,3‐thia­zole‐κ2N,N′)(oxydiacetato‐κ3O,O′,O′′)cobalt(II) trihydrate

The title compound, [Co(C₄H₄O₅)(C₆H₆N₄S₂)(H₂O)]·3H₂O, displays a distorted octa­hedral coordination geometry. The tridentate oxydiacetate dianion chelates the Cu^II atom in the meridional mode. In the crystal packing, hydro­philic and hydro­phobic layers are arranged in an alternating manner. In addition, a three‐dimensional hydrogen‐bonding framework and π–π stacking are present.     

Two new thiophosphoramide structures: N,N′,N′′‐tricyclohexylphosphorothioic triamide and O,O′‐diethyl (2‐phenylhydrazin‐1‐yl)thiophosphonate

The compound N,N′,N′′‐tricyclohexylphosphorothioic triamide, C₁₈H₃₆N₃PS or P(S)[NHC₆H₁₁]₃, (I), crystallizes in the space group Pnma with the molecule lying across a mirror plane; one N atom lies on the mirror plane, whereas the bond‐angle sum at the other N atom has a deviation of some 8° from the ideal value of 360° for a planar configuration. The orientation of the atoms attached to this nonplanar N atom corresponds to an anti orientation of the corresponding lone electron pair (LEP) with respect to the P=S group. The P=S bond length of 1.9785 (6) Å is within the expected range for compounds with a P(S)[N]₃ skeleton; however, it is in the region of the longest bond lengths found for analogous structures. This may be due to the involvement of the P=S group in N—H...S=P hydrogen bonds. In O,O′‐diethyl (2‐phenylhydrazin‐1‐yl)thiophosphonate, C₁₀H₁₇N₂O₂PS or P(S)[OC₂H₅]₂[NHNHC₆H₅], (II), the bond‐angle sum at the N atom attached to the phenyl ring is 345.1°, whereas, for the N atom bonded to the P atom, a practically planar environment is observed, with a bond‐angle sum of 359.1°. A Cambridge Structural Database [CSD; Allen (2002). Acta Cryst. B 58 , 380–388] analysis shows a shift of the maximum population of P=S bond lengths in compounds with a P(S)[O]₂[N] skeleton to the shorter bond lengths relative to compounds with a P(S)[N]₃ skeleton. The influence of this difference on the collective tendencies of N...S distances in N—H...S hydrogen bonds for structures with P(S)[N]₃ and P(S)[O]₂[N] segments were studied through a CSD analysis.     

{μ‐N,N′‐Bis[2‐(dimethylamino)ethyl]oxamidato(2–)‐κ6N,N′,O′:N′′,N′′′,O}bis[(2,2′‐bipyridine‐κ2N,N′)copper(II)] bis(perchlorate)

In the crystal structure of the title complex, [Cu₂(C₁₀H₂₀N₄O₂)(C₁₀H₈N₂)₂](ClO₄)₂, the deprotonated dmaeoxd²⁻ ligand {H₂dmaeoxd is N,N′‐bis[2‐(dimethylamino)ethyl]oxamide} occupies an inversion centre at the mid‐point of the central C—C bond and is thus in a trans conformation. The two Cu^II atoms are located in slightly distorted square‐based pyramidal environments. The binuclear units interact with each other viaπ–π interactions to form a one‐dimensional chain extending in the c direction.     

μ‐{N,N′‐Bis[2‐(dimethyl­amino)ethyl]oxamidato(2–)}‐1κ2O,O′:2κ4N,N′,N′′,N′′′‐bis­(4,4′‐dimethyl‐2,2′‐bipyridine‐1κ2N,N′)dinickel(II) bis­(perchlorate)

In the crystal structure of the title complex, [Ni₂(C₁₀H₂₀N₄O₂)(C₁₂H₁₂N₂)₂](ClO₄)₂ or [Ni(dmaeoxd)Ni(dmbp)₂](ClO₄)₂ {H₂dmaeoxd is N,N′‐bis­[2‐(dimethyl­amino)ethyl]oxamide and dmbp is 4,4′‐dimethyl‐2,2′‐bipyridine}, the deprotonated dmaeoxd²⁻ ligand is in a cis conformation and bridges two Ni^II atoms, one of which is located in a slightly distorted square‐planar environment, while the other is in an irregular octa­hedral environment. The cation is located on a twofold symmetry axis running through both Ni atoms. The dmaeoxd²⁻ ligands inter­act with each other via C—H⋯O hydrogen bonds and π–π inter­actions, which results in an extended chain along the c axis.     

(Aqua‐2κO)bis(2,2′‐bipyridine‐1κ2N,N′){μ‐N‐[3‐(dimethylamino)propyl]‐N′‐(2‐oxidophenyl)oxamidato(3−)‐1:2κ2O,O′:κ4O′′,N,N′,N′′}copper(II)nickel(II) perchlorate

The title complex, [CuNi(C₁₃H₁₆N₃O₃)(C₁₀H₈N₂)₂(H₂O)]ClO₄, has a cis‐oxamide‐bridged heterobinuclear cation, with a Cu...Ni separation of 5.3297 (6) Å, counterbalanced by a disordered perchlorate anion. The Cu^II and Ni^II cations are located in square‐pyramidal and octahedral coordination environments, respectively. The complex molecules are assembled into a three‐dimensional supramolecular structure through hydrogen bonds and π–π stacking interactions. The influence of the two types of metal cation on the supramolecular structure is discussed.     

Synthesis and insecticidal evaluation of N‐tert‐butyl‐N′‐thio[O‐(1‐methylthioethylimino)‐N″‐methylcarbamate]‐N,N′‐diacylhydrazines

A series of novel N‐tert‐butyl‐N′‐thio[O‐(1‐methylthioethylimino)‐N″‐methylcarbamate]‐N,N′‐diacylhydrazines were synthesized by the reaction of chlorosulfenyl[O‐(1‐methylthioethylimino)‐N‐methylcarbamate] with N‐tert‐butyl‐N,N′‐diacylhydrazine in the presence of sodium hydride. The reaction of sulfur dichloride with O‐(1‐methylthioethylimino)‐N‐methylcarbamate (Methomyl) in the presence of pyridine to yield chlorosulfenyl[O‐(1‐methylthioethylimino)‐N‐methylcarbamate] was reported for the first time. X‐ray single crystal diffraction of N‐tert‐butyl‐N′‐thio[O‐(1‐methylthioethylimino)‐N″‐methylcarbamate]‐N,N′‐dibenzoylhydrazine demonstrated that the parent compounds N‐tert‐butyl‐N,N′‐dibenzoylhydrazine and O‐(1‐methylthioethylimino)‐N‐methylcarbamate were combined by N S N band to give the product. Their larvicidal activities against Oriental armyworm and Aphis laburni were evaluated. All of them exhibited excellent larvicidal activities against Oriental armyworm, with some of them showing higher larvicidal activities than the parent diacylhydrazines. Toxicity assays indicated that the products show knockdown activity for O‐(1‐methylthioethylimino)‐N‐methylcarbamate at higher concentration and insect growth regulators' activities of diacylhydrazines at lower concentrations. At the same time, the products possess insecticidal activities against the aphids. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:631–636, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20360     

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.     

O‐Ethyl and O‐methyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d‐glucopyranosyl)thiocarbamate

In both the title structures, O‐ethyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d ‐gluco­pyran­osyl)­thio­carbam­ate, C₁₇H₂₅NO₁₀S, and O‐methyl N‐(2,3,4,6‐tetra‐O‐acetyl‐β‐d ‐gluco­pyran­osyl)­thiocar­bam­ate, C₁₆H₂₃NO₁₀S, the hexo­pyran­osyl ring adopts the ⁴C₁ conformation. All the ring substituents are in equatorial positions. The acetoxy­methyl group is in a gauche–gauche conformation. The S atom is in a synperi­planar conformation, while the C—N—C—O linkage is antiperiplanar. N—H?O intermolecular hydrogen bonds link the mol­ecules into infinite chains and these are connected by C—H?O interactions.     

Poly[(N,N‐dimethylformamide‐κO)(μ3‐4,4′‐ethylenedibenzoato‐κ5O,O′:O′:O′′,O′′′)(pyrazino[2,3‐f][1,10]phenanthroline‐κ2N8,N9)lead(II)]

In the title Pb^II coordination polymer, [Pb(C₁₆H₁₀O₄)(C₁₄H₈N₄)(C₃H₇NO)]_n, each Pb^II atom is eight‐coordinated by two chelating N atoms from one pyrazino[2,3‐f][1,10]phenanthroline (L) ligand, one dimethylformamide (DMF) O atom and five carboxylate O atoms from three different 4,4′‐ethylenedibenzoate (eedb) ligands. The eedb dianions bridge neighbouring Pb^II centres through four typical Pb—O bonds and one longer Pb—O interaction to form a two‐dimensional structure. The C atoms from the L and eedb ligands form C—H...O hydrogen bonds with the O atoms of eedb and DMF ligands, which further stabilize the structure. The title compound is the first Pb^II coordination polymer incorporating the L ligand.     

μ‐Acetato‐1:2κ2O:O′‐diacetato‐1κ2O,O′;2κO‐bis(di‐2‐pyridylamine)‐1κ2N,N′;2κ2N,N′‐isothiocyanato‐2κN‐dicopper(II)

In the title dinuclear acetate‐bridged complex, [Cu₂(C₂H₃O₂)₃(NCS)(C₁₀H₉N₃)₂], the two Cu atoms are five‐coordinated, with a basal plane consisting of two N atoms of a di‐2‐pyridylamine (dpyam) ligand and two O atoms of two different acetate ligands. The axial positions of these Cu atoms are coordinated to N and O atoms from thio­cyanate and acetate mol­ecules, respectively, leading to a distorted square‐pyramidal geometry with τ values of 0.30 and 0.22. Both Cu^II ions are linked by an acetate group in the equatorial–equatorial positions and have syn–anti bridging configurations. Hydrogen‐bond inter­actions between the amine H atom and the coordinated and uncoordinated O atoms of the acetate anions generate an infinite one‐dimensional chain.     

μ‐Oxo‐bis{[(6‐hydroxy­methyl‐2‐pyridyl­methyl)­bis(2‐pyridyl­methyl)­amine‐κ5N,N′,N′′,N′′′,O]­iron(III)} tetrakis­(perchlorate)

The novel μ‐oxo‐diiron complex [Fe₂O(BPHPA)₂](ClO₄)₄ [BPHPA is (6‐hydroxy­methyl‐2‐pyridyl­methyl)­bis(2‐pyridyl­methyl)­amine, C₁₉H₂₀N₄O], contains a binuclear centrosymmetric [Fe₂O(BPHPA)₂]⁴⁺ cation (the bridging O atom lies on an inversion centre) and four perchlorate anions. Each iron ion is coordinated by four N atoms [Fe—N = 2.117 (5)–2.196 (5) Å] and one O atom [Fe—O = 2.052 (5) Å] from a BPHPA ligand, and by one bridging oxo atom [Fe—O = 1.7896 (9) Å], forming a distorted octahedron. There are hydrogen bonds between the hydroxy group and perchlorate O atoms [O—H·O = 2.654 (7) Å].     

{2‐[(3‐Amino­propyl)­amino­propyl­imino­methyl]­imidazol­ato‐N,N′,N′′,N′′′}­(methanol‐O)­copper(II) per­chlorate

In the title compound, [Cu(C₁₀H₁₈N₅)(CH₄O)]ClO₄, four N atoms from the deprotonated ligand derived from bis(3‐amino­propyl)­amine and 2‐imidazole­carbox­aldehyde are coordinated to the Cu atom. The four N atoms occupy equatorial positions with Cu—N bond distances ranging from 1.998 (2) to 2.046 (3) Å. The methanol O atom occupies one axial position with a Cu—O bond distance of 2.295 (2) Å.