Oligonucleosides with a Nucleobase‐Including Backbone,Part 7

The conformational analysis of 7 was carried out in (D₆)DMSO and in mixtures of (D₆)DMSO and CDCl₃ to evaluate the syn/anti conformations, relevant to the pairing propensity of this type of nucleotide analogue. The HO−C(5′) of unit I and of unit II of the dimer 7 form an intramolecular H‐bond to N(3). In (D₆)DMSO, the C(5′)−OH⋅⋅⋅N(3) H‐bond in unit I is partially broken, while that in unit II persists to a larger extent. The syn conformation prevails for unit I and particularly for unit II. The furanosyl moieties adopt predominantly a 2′‐endo conformation that is largely independent of the solvent.     

Synthesis of Conformationally Restricted Carbocyclic Nucleosides: The Role of the O(4′)-Atom in the Key Hydration Step of Adenosine Deaminase

Conformationally restricted carbocyclic nucleosides with either a northern(N)-type conformation, i.e., N-type 2′-deoxy-methanocarba-adenosine 8 ((N)MCdAdo), or a southern(S)-type conformation, i.e. S-type 2′-deoxy-methanocarba-adenosine 9 , ((S)MCdAdo), were used as substrates for adenosine deaminase (ADA) to assess the enzyme's preference for a fixed conformation relative to the flexible conformation represented by the carbocyclic nucleoside aristeromycin ( 10 ). Further comparison between the rates of deamination of these compounds with those of the two natural substrates adenosine (Ado; 1 ) and 2′-deoxyadenosine (dAdo; 2 ), as well as with that of the conformationally locked nucleoside LNA-Ado ( 11 ), which, like the natural substrates, has a furanose O(4′) atom, helped differentiate between the roles of the O(4′) anomeric effect and sugar conformation in controlling the rates of deamination by ADA. Differences in rates of deamination as large as 10000 can be attributed to the combined effect of the O(4′) atom and the enzyme's preference for an N-type conformation. The hypothesis proposed is that ADA's preference for N-type substrates is not arbitrary; it is rather the direct consequence of the conformationally dependent O(4′) anomeric effect, which is more efficient in N-type conformers in promoting the formation of a covalent hydrate at the active site of the enzyme. The formation of a covalent hydrate at the active site of ADA precedes deamination. A new and efficient synthesis of the important carbobicyclic template 14a , a useful intermediate for the synthesis of (N)MCdAdo ( 8 ) and other conformationally restricted nucleosides, is also reported.     

The 7‐bromo derivative of 2‐amino‐2′‐deoxytubercidin fluorinated at the sugar moiety

The title compound, 2,4‐diamino‐5‐bromo‐7‐(2‐deoxy‐2‐fluoro‐β‐d ‐arabinofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine, C₁₁H₁₃BrFN₅O₃, shows two conformations of the exocyclic C4′—C5′ bond, with the torsion angle γ (O5′—C5′—C4′—C3′) being 170.1 (3)° for conformer 1 (occupancy 0.69) and 60.7 (7)° for conformer 2 (occupancy 0.31). The N‐glycosylic bond exhibits an anti conformation, with χ = −114.8 (4)°. The sugar pucker is N‐type (C3′‐endo; ³T₄), with P = 23.3 (4)° and τ_m = 36.5 (2)°. The compound forms a three‐dimensional network that is stabilized by several intermolecular hydrogen bonds (N—H...O, O—H...N and N—H...Br).     

Synthese von Nucleosiden aus 2-substituierten Imidazolen

Synthesis of 2-Substituted Imidazole Nucleosides Condensation of the trimethylsilyl derivatives of 2-substituted diethyl and dimethyl imidazole-4,5-dicarboxylates ( 3–5 and 7–9 ) with 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D -ribofuranose ( 2 ) in the presence of trimethysilyl trifluoromethanesulfonate provided the 2-substituted diethyl and dimethyl 1-(2′,3′, 5′-tri-O-benzoyl-β-D -ribofuranosyl)imidazole-4, 5-dicarboxylates 10–15 . These were treated with ammonia to afford the 2-substituted 1-(β-D -ribofuranosyl)imidazole-4,5-dicarboxamides 16–21 . Treatment of 2-methyl-( 16 ) and 2-ethyl-1-(β-D -ribofuranosyl)imidazole-4,5-dicarboxamide ( 17 ) with fuming nitric acid in oleum at ?30° yielded the nitric acid esters 23 and 24 . Besides the esterification of the sugar hydroxyl groups one H-atom of the imidazolecarboxamide function at C(5) in these nucleosides was also substituted by the NO₂ group. The conformations in solution of 16 and 23 have been determined by ¹H- and ¹³C-NMR. spectroscopy. These studies indicate that the nucleosides exist in dimethyl-sulfoxide solution preferentially in the S-gg-syn-conformation ( 16 ) and N-gt-conformation ( 23 ). In the crystal structure of nucleoside 23 , the ribose was found to be in the O(1′)_endo, C(1′)_exo twist conformation. The conformation about C(4′), C(5′) is gauche-trans and the molecule exists in the syn form.     

Synthesis and Crystal Structures of O‐2′,3′‐Cyclic Cyclopentanone and Cyclohexanone Ketals of the Cytostatic 5‐Fluorouridine

The synthesis of two O‐2′,3′‐cyclic ketals, i.e., 5 and 6 , of the cytostatic 5‐fluorouridine ( 2 ), carrying a cyclopentane and/or a cyclohexane ring, respectively, is described. The novel compounds were characterized by ¹H‐, ¹⁹F‐, and ¹³C‐NMR, and UV spectroscopy, as well as by elemental analyses. Their crystal structures were determined by X‐ray analysis. Both compounds 5 and 6 show an anti‐conformation at the N‐glycosidic bond which is biased from +ac to +ap compared to the parent nucleoside 2 . The sugar puckering is changed from ^2′E to _3′E going along with a reduction of the puckering amplitude τ_m by ca. 10–13° due to the ketalization. The conformation about the sugar exocyclic bond C(4′)? C(5′) of 5 and 6 remains unchanged, i.e., g⁺, compared with compound 2 .     

7‐Deaza‐2,8‐diaza­adenosine

In the title compound [systematic name: 4‐amino‐7‐(β‐d ‐ribofuranos­yl)‐7H‐pyrazolo[3,4‐d][1,2,3]triazine], C₉H₁₂N₆O₄, the torsion angle of the N‐glycosylic bond is high anti [χ = −83.2 (3)°]. The ribofuran­ose moiety adopts the C2′‐endo–C1′‐exo (²T₁) sugar conformation (S‐type sugar pucker), with P = 152.4° and τ_m = 35.0°. The conformation at the C4′—C5′ bond is +sc (gauche,gauche), with the torsion angle γ = 52.0 (3)°. The compound forms a three‐dimensional network that is stabilized by several hydrogen bonds (N—H⋯O, O—H⋯N and O—H⋯O).     

Synthesis and properties of conformationally locked 1,3-bisalkyl-7-deazaxanthine 2′-deoxy-d-ribofuranosides

1,3-Dimethyl-7-deazaxanthine 2′-deoxyribofuranosides 1a and 6a and their N-3 isopropyl congeners 1b and 6b have been prepared employing the nucleobase anions 7a or 7b and 2-deoxy-3,5-di-O-(p-toluoyl)-α-D-erythropentofuranosyl chloride ( 8 ) upon glycosylation. The reaction was not stereoselective as found in case of other pyrrolo[2,3-d]pyrimidine nucleosides induced by the bulky N-3 substituent. Configuration of anomers was established by ¹H-nmr nOe difference spectroscopy. Those data also indicated that the conformation around the N-glycosylic bond was locked by the bulky N-3 substituent. Contrary to the purine nucleoside such as wyosine ( 2a ) the hydrolytic stability of the N-glycosylic bond of the pyrrolo[2,3-d]pyrimidine nucleosides was increased by N-3 alkylation. Moreover, it was shown by ¹⁵N-nmr spectroscopy that different to purine nucleosides the aglycon was not protonated in acidic medium. As a result the N-glycosylic bond hydrolysis did not follow an A-1 but an A-2 mechanism.     

The α‐d anomer of 5‐aza‐7‐deaza‐2′‐deoxyguanosine

In the monohydrate of 2‐amino‐8‐(2‐deoxy‐α‐d ‐erythro‐pento­furan­osyl)‐8H‐imidazo­[1,2‐a]­[1,3,5]­triazin‐4‐one, C₁₀H₁₃N₅O₄·H₂O, denoted (I) or αZ_d, the conformation of the N‐gly­cosyl­ic bond is in the high‐anti range [χ = 87.5 (3)°]. The 2′‐deoxy­ribo­furan­ose moiety adopts a C2′‐endo,C3′‐exo(^2′T_3′) sugar puckering (S‐type sugar) and the conformation at the C4′—C5′ bond is ?sc (trans).     

Stereochemical Analysis of an Aromatic Triplet Di-π-methane Rearrangement

It is shown that (−)-(S)-N,N-dimethyl-2-(1′-methylallyl)aniline ((−)-(S)- 4 ), on direct irradiation in MeCN at 20°, undergoes in its lowest-lying triplet state an aromatic di-π-methane (ADPM) rearrangement to yield (−)-(1′R,2′R)- and (+)-(1′R,2′S)-N,N-dimethyl-2-(2-methylcyclopropyl)aniline ((−)-trans- and (+)-cis- 7 ) in an initial trans/cis ratio of 4.71 ± 0.14 and in optical yields of 28.8 ± 5.2% and 15 ± 5%, respectively. The ADPM rearrangement of (−)-(S)- 4 to the trans- and cis-configurated products occurs with a preponderance of the path leading to retention of configuration at the pivot atom (C(1′) in the reactant and C(2′) in the products) for (−)-trans- 7 and to inversion of configuration for (+)-cis- 7 , respectively. The results can be rationalized by assuming reaction paths which involve the occurrence of discrete 1,4- and 1,3-diradicals (cf. Schemes 10, 12, and 13). A general analysis of such ADPM rearrangements which allows the classification of these photochemical reactions in terms of borderline cases is presented (Scheme 14). It is found that the optical yields in these ‘step-by-step’ rearrangements are determined by the first step, i.e. by the disrotatory bond formation between C(2) of the aromatic moiety and C(2′) of the allylic side chain leading to the generation of the 1,4-diradicals. Moderation of the optical yields can occur in the ring closure of the 1,3-diradicals to the final products, which may take place with different trans/cis-ratios for the individual 1,3-diradicals. Compounds (−)-trans- 7 as well as (+)-cis- 7 easily undergo the well-known photochemical trans/cis-isomerization. It mainly leads to racemization. However, a small part of the molecules shows trans/cis-isomerization with inversion of configuration at C(1′), which is best explained by a photochemical cleavage of the C(1′)–C(3′) bond.     

13C nuclear magnetic resonance spectroscopy of selected adenine nucleosides: Structural correlation and conformation about the glycosidic bond

Structural correlations have been carried out from ¹³C chemical shifts (δ) and by analysis of ¹J(CH) coupling constants, and the conformation about the glycosidic bond has been studied by means of the ³J(CH) vicinal coupling constants between C-8 and H-1′ of some adenine nucleosides such as adenosine (Ado), N(7)-β-D-ribofuranosyladenine (N(7)-Ado), N(9)- and N(7)-β-D-xylofuranosyladenine (N(9)-xylAde and N(7)-xylAde), N(9)-(3-chloro-3-deoxy-β-D-xylofuranosyl)adenine (3′-Cl-xylAde) and N(9)-(2-chloro-2-deoxy-β-D-arabinofuranosyl)adenine (2′-Cl-araAde). The analysis of the influence on δ¹³C of the nature and configuration of the substituent in the carbohydrate fragment of the molecule has revealed two types of effects, namely, 1,2-cis and 1,2-trans. This approach, as well as the ³J(CH) values and the analysis of the C-3′-endo?C-2′-endo equilibrium of the carbohydrate fragment of nucleosides, and circular dichroism (CD) data, provides important information on the conformation about the glycosidic bond. The magnitudes of ³J(C-4, H) are indicative of the position of attachment of the carbohydrate fragment to the heterocyclic base.     

Regioisomeric 4‐nitroindazole N1‐ and N2‐(β‐d‐ribonucleosides)

The structures of the isomeric nucleosides 4‐nitro‐1‐(β‐d ‐ribo­furan­osyl)‐1H‐indazole, C₁₂H₁₃N₃O₆, (I), and 4‐nitro‐2‐(β‐d ‐ribo­furan­osyl)‐2H‐indazole, C₁₂H₁₃N₃O₆, (II), have been determined. For compound (I), the conformation of the gly­cosylic bond is anti [χ = −93.6 (6)°] and the sugar puckering is C2′‐exo–C3′‐endo. Compound (II) shows two conformations in the crystalline state which differ mainly in the sugar pucker; type 1 adopts the C2′‐endo–C3′‐exo sugar puckering associated with a syn base orientation [χ = 43.7 (6)°] and type 2 shows C2′‐exo–C3′‐endo sugar puckering accompanied by a somewhat different syn base orientation [χ = 13.8 (6)°].     

A locked derivative of 8‐aza‐7‐deazaadenosine

The title compound [systematic name: (1S,3S,4R,7S)‐3‐(4‐amino‐1H‐pyrazolo[3,4‐d]pyrimidin‐1‐yl)‐1‐hydroxymethyl‐2,5‐dioxabicyclo[2.2.1]heptan‐7‐ol], C₁₁H₁₃N₅O₄, belongs to a family of nucleosides with modifications in both the sugar and nucleobase moieties: these modifications are known to increase the thermodynamic stability of DNA and RNA duplexes. There are two symmetry‐independent molecules in the asymmetric unit that differ significantly in conformation, and both exhibit a high‐anti conformation about the N‐glycosidic bond, with χ torsion angles of −85.4 (3) and −87.4 (3)°. The sugar C atom attached to the nucleobase N atom is −0.201 (4) and 0.209 (4) Å from the 8‐aza‐7‐deazaadenine skeleton plane in the two molecules. The molecules are assembled into layers via hydrogen bonds and π–π stacking interactions between the modified nucleobases.     

N8‐(2′‐O‐Methyl­ribofuranos­yl)‐8‐aza‐7‐deaza­adenine monohydrate

In the title compound, 4‐amino‐2‐(2‐O‐methyl‐β‐d ‐ribofuranos­yl)‐2H‐pyrazolo[3,4‐d]pyrimidine monohydrate, C₁₁H₁₅N₅O₄·H₂O, the conformation of the N‐glycosylic bond is syn [χ = 20.1 (2)°]. The ribofuran­ose moiety shows a C3′‐endo (³T₂) sugar puckering (N‐type sugar), and the conformation at the exocyclic C4′—C5′ bond is −ap (trans). The nucleobases are stacked head‐to‐head. The three‐dimensional packing of the crystal structure is stabilized by hydrogen bonds between the 2′‐O‐methyl­ribonucleosides and the solvent mol­ecules.     

(6R,9′Z)-Neoxanthin: Synthese,Schmelzverhalten, Spektren und Konformationsberechnungen

(6R,9′Z)-Neoxanthin: Synthesis, Physical Properties, Spectra, and Calculations of Its Conformation in Solution The synthesis of pure and crystalline (9′Z)-neoxanthin ( 6 ) is described. MnO₂ Oxidation of (9Z)-C₁₅-alcohol 7 at room temperature produces a mixture 8/9 of (9Z)- and (9E)-aldehydes. Predominant formation of the required (9Z)-aldehyde 8 is achieved by performing the oxidation at ? 10°. Condensation of 8 with the mono-Li salt of the symmetrical C₁₀-diphosphonate 10 gave the (9Z)-C₂₅-monophosphonate 11 . The Wittig-Horner condensation of 10 with the allenic C₁₅-aldehyde 1b , under selected conditions allows the preparation of pure and crystalline (9′Z)-15,15′-didehydroneoxanthin ( 12 ) and, after subsequent semireduction, of crystalline (15Z,9′Z)-neoxanthin ( 13 ). Thermal isomerisation of a AcOEt solution of 13 at 95° yields preferentially (9′Z)-neoxanthin ( 6 ). Our crystalline sample shows the highest ?-values in the UV/VIS spectra ever recorded. The CD spectra display a pronounced similarity with those of corresponding violaxanthin isomers. In contrast to the (all-E)-isomer 5 , (9′Z)-neoxanthin undergoes very little isomerisation when heated to its melting point. For comparison purposes, a crystalline probe of 6 is also isolated from lawn mowings. Extensive ¹H-and ¹³C-NMR investigations at 600 MHz of a (D₆)benzene solution using 2D-experiments such as COSY, TOCSY, ROESY, HMBC, and HMQC techniques permit the unambiguous assignment of all signals. Force-field calculations of a model system of 6 indicate the presence of several interconverting conformers of the violaxanthin end group, 66% of which possess a pseudoequatorial and 34% a pseudoaxial OH? C(3′). The torsion angle (ω₁) around the C(6′)? C(7′) bond, known to be of prime importance for the shape of the CD spectra, varies with values of 87° for 55% and 263° for 45% of the molecules. Therefore, the molecules clearly display a preference for the ‘syn’-position of the C(7′)?C(8′) bond and the epoxy group. Unexpectedly, the double bonds of C(7′)?C(8′) and C(9′)?C(10′) are not coplanar. The deviation amounts to ± 20°, both in the ‘syn’ - and the ‘anti’-conformation.     

两个新颖的联环十二烷衍生物的合成及结构表征

2-（2＇-Oxo-3＇-oximidocyclododecyl） cyclododecanone （1） and 2-（1＇-hydroxylcyclododecyl） cyclododecanone （2） were synthesized and characterized. The conformation analysis was carried out based on the NMR, molecular mechanics calculation and X-ray diffraction. The conformation of two cyclododecyl moieties of both 1 and 2 was found to be the [3333]-2-one or [3333] square conformation both in the crystal state and the solution. The dihedral angle between carbonyl and the oxime double bond of the ring B is 180°in the crystal of 1. The protons or hydroxyl group of carbon atoms to link the two cyclododecyl moieties of 1 and 2 constitute dihedral angles of 174°in the crystal, and 175°in the solution, and the C-C 6 bond between two cyclododecyl moieties can not freely rotate in the solid state and the solution. In addition, compound 2 was the first example of a-comer-anti-monosubstituted cyclododecanone. synthesis     

8‐Aza‐7‐deaza‐7‐propynyladenosine methanol solvate

In the title compound, 4‐amino‐3‐propynyl‐1‐(β‐d ‐ribofur­anosyl)‐1H‐pyrazolo[3,4‐d]pyrimidine methanol solvate, C₁₃H₁₅N₅O₄·CH₃OH, the torsion angle of the N‐glycosylic bond is between anti and high‐anti [χ = −101.8 (5)°]. The ribofuranose moiety adopts the C3′‐endo (³T₂) sugar conformation (N‐type) and the conformation at the exocyclic C—C bond is +sc (gauche, gauche). The propynyl group is out of the plane of the nucleobase and is bent. The compound forms a three‐dimensional network which is stabilized by several hydrogen bonds (O—H·O and O—H·N). The nucleobases are stacked head‐to‐tail. The methanol solvent mol­ecule forms hydrogen bonds with both the nucleobase and the sugar moiety.     

Synthèse et désamination enzymatique des C-hydroxyméthyl-3′- et C-méthyl-3′-β-D-xylofurannosyl-9-adénines

Synthesis and enzymatic deamination of 3′-C-hydroxymethyl- and 3′-C-methyl-β-D -xylofuranosyl-9-adenines The title compounds have been prepared by classical synthetic steps after having optimized the nature of the blocking groups. Both nucleosides were found to be substrates of adenosine aminohydrolase which proved that C(3′)-branched-chain sugar nucleosides can be deaminated when the branched-chain is exo (trans relative to the base) if a suitably disposed hydroxy group is available on the endo side of the furanose ring.     

7‐Cyclopropyl‐2′‐deoxytubercidin: a carbocyclic side‐chain derivative of 7‐deaza‐2′‐deoxyadenosine

The title compound {systematic name: 4‐amino‐5‐cyclopropyl‐7‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine}, C₁₄H₁₈N₄O₃, exhibits an anti glycosylic bond conformation, with the torsion angle χ = −108.7 (2)°. The furanose group shows a twisted C1′‐exo sugar pucker (S‐type), with P = 120.0 (2)° and τ_m = 40.4 (1)°. The orientation of the exocyclic C4′—C5′ bond is ‐ap (trans), with the torsion angle γ = −167.1 (2)°. The cyclopropyl substituent points away from the nucleobase (anti orientation). Within the three‐dimensional extended crystal structure, the individual molecules are stacked and arranged into layers, which are highly ordered and stabilized by hydrogen bonding. The O atom of the exocyclic 5′‐hydroxy group of the sugar residue acts as an acceptor, forming a bifurcated hydrogen bond to the amino groups of two different neighbouring molecules. By this means, four neighbouring molecules form a rhomboidal arrangement of two bifurcated hydrogen bonds involving two amino groups and two O5′ atoms of the sugar residues.     

7‐Deaza‐2′‐deoxyinosine: a nucleoside showing ambiguous base‐pairing properties against the four canonical DNA constituents

The title compound [systematic name: 7‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐3,7‐dihydro‐4H‐pyrrolo[2,3‐d]pyrimidin‐4‐one], C₁₁H₁₃N₃O₄, represents an acid‐stable derivative of 2′‐deoxyinosine. It exhibits an anti glycosylic bond conformation, with a χ torsion angle of 113.30 (15)°. The furanose moiety adopts an S‐type sugar pucker ⁴T₃, with P = 221.8 (1)° and τ_m = 40.4 (1)°. The conformation at the exocyclic C4′—C5′ bond of the furanose ring is ap (trans), with γ = 167.14 (10)°. The extended structure forms a three‐dimensional hydrogen‐bond network involving O—H...O, N—H...O and C—H...O hydrogen bonds. The title compound forms an uncommon hydrogen bond between a CH group of the pyrrole system and the ring O atom of the sugar moiety of a neighbouring molecule.     

Synthesis and conformational properties of 2′-deoxy-2′-methylthio-pyrimidine and -purine nucleosides: Potential antisense applications

A convenient and shorter synthesis of 2′-deoxy-2′-methylthiouridine analogs 5 , ?5-methyluridine 6 , -cyti-dine 15 , ?5-methylcytidine 16 , -adenosine 27 and -guanosine 34 was accomplished. Successful conversion of ribonucleosides (5-methyl U, U, A, G) into the corresponding 2′-substituted nucleosides involves nucleophilic displacement (S_N2) of an appropriate leaving group at the 2′-position by methanethiol, a soft nucleophile. Reaction between 2,2′-anhydrouridine and methanethiol in the presence of N¹,N¹,N³,N³-tetramethylguani-dine in N,N-dimethylformamide gave 5 , in 75% yield. Preparation of 6 by a similar route was described. Acylated 5 and 6 were transformed into their triazole derivatives, which on ammonolysis furnished 15 and 16 , respectively in good yield. Similarly, tetraisopropyldisiloxanyl (TIPS) protected 2′-O-aratriflates- of-adenosine and -guanosine reacted with methanethiol in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene at - 25°, followed by deblocking of the TIPS protecting group furnished 27 and 34 , respectively. The confor-mational flexibility (N/S equilibrium) of the sugar moiety in nucleosides 5 , 15 , 27 and 34 was studied utilizing nmr spectroscopy, suggesting that the 2′-methylthio group influenced the sugar conformation to adopt a rigid S-pucker in all cases. The extra stiffness of the sugar moiety in these analogs is believed to be due to the electronegativity of the substituent and the steric bulk. The usefulness of these nucleosides to prepare uniformly modified 2′-deoxy-2′-methylthio oligonucleotides for antisense therapeutics is proposed.