Synthesis, NMR spectroscopy, and crystal structure of [9](<i>N</i>6,9)-6-aminopurinophane

Capretta, Alfredo; Hunter, Howard N.; Frampton, Christopher S.; Bell, Russell A.

doi:10.1139/v93-014

Cited by 5 publications

(5 citation statements)

References 16 publications

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“…The signal dispersion observed for C12 alkane linkers of the hairpins is similar to that reported for the methylene protons of 6-aminopurine cyclophanes in which a C8−C10 alkane chain is connected to nitrogen N9 and the amino group − and is consistent with a structure in which the upfield protons lie in the shielding region of the adjacent AT base pair . However, the maximum upfield shifts are smaller for the hairpins than for the purine cyclophanes.…”

Section: Resultssupporting

confidence: 81%

“…Dodecane fits into molecular capsules that are too short to accommodate a fully extended conformation by adopting helical conformations having multiple gauche bonds, whereas the shorter n- decane adopts an extended conformation. , Weak alkane-arene interactions are reported to favor folded conformations for C 12 in benzene but extended conformations in 1-chloronaphthalene . Attaching the ends of an alkane chain to a rigid scaffold results in gauche-rich conformations for most cylcophanes − but an all-anti conformation for a teropyrenophane with a stretched alkane linker . Thus n- alkanes can readily adapt their conformations to their environment.…”

Section: Introductionmentioning

confidence: 99%

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Conformation of a Dodecane DNA Hairpin Linker. Multiple Gauche Bonds Cover the Bases

Siegmund¹,

Hariharan²,

Lewis³

2011

J. Phys. Chem. B

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Alkane linkers derived from α,ω-alkane diols have been employed for the preparation of DNA mini-hairpins, which are suitable for studies of the spectroscopy and photochemistry of short base pair domains. The solution structure of a DNA hairpin having a n-dodecane linker and six AT base pairs has been determined using (1)H NMR data with restrained molecular dynamics. The chemical shifts of the 12 diastereotopic pairs of linker protons show a distribution of values depending on their locations within the shielding region of the ring-currents of the adjacent base pair. Chemical shifts calculated from the mean NMR solution structure show the same overall distribution, but with larger absolute values for the upfield shifts. The C12 linker lies approximately parallel to the adjacent base pair and adopts a highly curved structure having an average of 4-5 gauche C-C bonds, in contrast to a modeled B-DNA structure which has a more fully extended alkane chain. This curved structure results in an average P-P distance of 15.4 Å, substantially shorter than the 17.7 Å average distance for B-DNA. This structure appears to maximize the hydrophobic interactions between the linker and the adjacent base pair. Partial NMR assignments for the C12 linker in a second hairpin having a different base-pair sequence indicates that it adopts a similar curved geometry having multiple gauche bonds. The hairpin base pair domain adopts a B-DNA geometry in which the AT base pair adjacent to the linker displays Watson-Crick base pairing, in spite of the relatively short P-P distance. The terminal bases-pair shows evidence of extensive end-fraying. The four interior base pairs display a normal B-DNA geometry, thus providing good models for base pair domains embedded in longer duplexes.

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Section: Resultssupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Conformation of a Dodecane DNA Hairpin Linker. Multiple Gauche Bonds Cover the Bases

Siegmund¹,

Hariharan²,

Lewis³

2011

J. Phys. Chem. B

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“…Although the method of Castro and co-workers in (6) for preparing azido-alcohols worked well in the synthesis of 2, the price of hexamethylphosphorous triamide (HMPT) coupled with the diminished yields upon the "scaling-up" of the reaction prompted the search for a new preparative route to 10-azido-l-decanol (see Scheme 1,5). Kang, Kim, and Moon describe a simple method for the preparation of o-bromo-alcohols from u,o-diols (7).…”

Section: Synthesismentioning

confidence: 99%

“…Ultimately, the implementation of this two-step procedure allowed for efficient access to large quantities of pure, low-cost azido-alcohols. ~t t a c h m e n t of the methylene bridge to the purine was then achieved using the protocol described previously (5). As shown in Scheme 1, a Mitsunobu reaction involving 6-chloropurine and 10-azido-l-decanol allows for alkylation at N9 to yield 6.…”

Section: Synthesismentioning

confidence: 99%

“…1, spectrum (c)), the multiple signals within the aromatic region revealed the presence of multiple conformations. The two major forms likely arise from the anti-syn isomerization about the N b C 6 bond and may be compared with those seen in the low temperature [9](N6,9)-6-aminopurinophane NMR spectrum (5). The anti conformer is preferred by approximately 4: 1 over the syn orientation.…”

Section: Nmr Spectroscopymentioning

confidence: 99%

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Synthesis, NMR and ultraviolet spectroscopy of [10] (N6,9)-6-aminopurinophane; calculation of the chemical shifts in the [n](N6,9)-6-aminopurinophane series

Capretta¹,

Bell²

1995

Can. J. Chem.

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Abstract:[10](N6,9)-6-Aminopurinophane was prepared via a Mitsunobu reaction involving 6-chloropurine and 10-azido-1-decanol. Reduction of the azido moiety to an amine allowed for subsequent cyclization to the cyclophane. N6-Nonyladenine, 9-nonyladenine, and N6,9-dinonyladenine were also prepared using the established chemistry. Heating the [10](N6,9)-6-aminopurinophane to 90°C allowed for a complete assignment of the proton and carbon spectra, while cooling the sample to -77°C revealed additional isomers likely due to the anti-syn isomerization about the N6-C6 bond. A variable temperature proton NMR study revealed a AG,' of 59.4 2 5.5 kJ mol-' associated with the interchange between the two major conformers. The ultraviolet spectra of the [n](N6,9)-6-aminopurinophane series show a bathochromic shift and a hypochromic effect in the transitions as the methylene chain length decreases (i.e., n = 10 to 9 to 8). The aminopurinophanes are used to assess the relative merits of a semi-empirical model that allows for the calculation of the chemical shifts of the methylene bridge protons.Key words: synthesis of heterocyclophanes, variable temperature NMR, cyclophane conformational analysis, ultraviolet spectroscopy, calculation of chemical shift.Resume : On a prepare le [10](N6,9)-6-aminopurinophane via une reaction de Mitsunobu impliquant la 6-chloropurine et le 10-azidodkcan-1-01. La rCduction de la portion azido en amine a permis de rCaliser la cyclisation subsCquente en cyclophane. On a aussi prCparC les N6-nonyladCnine, 9-nonyladCnine et N6,9-dinonyladenine utilisant des mCthodes chimiques bien Ctablies. Par chauffage du [10](N6,9)-6-aminopurinophane B 90°C, on a pu faire une attribution complbte des spectres RMN du proton et du carbone alors que son refroidissement B -77°C a rCvClC la presence d'isombres additionnels qui sont probablement dus B une isomCrisation anti-syn autour de la liaison N G C 6 . Une ttude des spectres RMN du proton B temperature variable a permis d'Ctablir qu'un AG,' de 39,4 ? 5,5 kJ mol-' est associC B l'interconversion entre les deux conformkres principaux. Les spectres ultraviolets de la sCrie des [tz](N6,9)-6-aminopurinophanes montrent qu'une diminution de la chaine mCthylCnique (lorsque n passe de 10, B 9 et B 8) est associCe B un dCplacement bathochrome et L un effet hypochrome dans les transitions. On a utilisC les aminopurinophanes pour Cvaluer les mCrites relatifs d'un modble semi-empirique qui permet de calculer les deplacements chimiques des protons des ponts mCthylbnes. ..Mots elks : synthkse d'hCterocyclophanes, RMN B temperature variable, analyse conformationnelle des cyclophanes, spectroscopie ultraviolette, calcul des dCplacements chimiques.[Traduit par la rCdaction] Introductionanisotropy about these purine and pyrimidine systems could aid in thegssignment of ;he heterobase protons ii the 'H NMRThe shift to lower frequency of the heterobase protons in cerspectra of large oligomers. Furthermore, this information tain oligonucleotides is a well-documented phenomenon (1 1.could ...

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ChemInform Abstract: Synthesis, NMR Spectroscopy, and Crystal Structure of (9)(N6,9)‐6‐ Aminopurinophane.

et al. 1993

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Synthesis, NMR Spectroscopy, and Crystal Structure of (9)(N6,9)-6-Aminopurinophane.-The title compound (V) crystallizes at 173 K in the space group P21/n with Z = 8. Variable temp. 1H NMR spectra show the presence of two conformers below -25 • C. -(CAPRETTA, A.; HUNTER, H. N.; FRAMPTON, C. S.; BELL, R. A.; Can. J. Chem. 71 (1993) 1, 96-106; Dep. Chem., McMaster Univ., Hamilton, Ont. L8S 4M1, Can.; EN)

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Synthesis, NMR spectroscopy, and crystal structure of [9](N6,9)-6-aminopurinophane

Cited by 5 publications

References 16 publications

Conformation of a Dodecane DNA Hairpin Linker. Multiple Gauche Bonds Cover the Bases

Conformation of a Dodecane DNA Hairpin Linker. Multiple Gauche Bonds Cover the Bases

Synthesis, NMR and ultraviolet spectroscopy of [10] (N6,9)-6-aminopurinophane; calculation of the chemical shifts in the [n](N6,9)-6-aminopurinophane series

ChemInform Abstract: Synthesis, NMR Spectroscopy, and Crystal Structure of (9)(N6,9)‐6‐ Aminopurinophane.

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