Synthesis, C-13 NMR, and X-ray crystal structure of N6,N9-octamethylenepurinecyclophane

Abstract

). The synthesis and structure determination of N6,N9-octamethylenepurine cyclophane by single crystal X-ray diffraction is reported. The cyclophane was prepared from 6-chloropurine a i d 8-aminooctanoic acid as starting materials. The aminooctyl fragment was first attached to N9 of 6-chloropurine by means of the Mitsunobu reaction and cyclization to the cyclophane effected by nucleophilic attack of the amino group at the C6 position and displacement of chloride ion. Reversing the reaction strategy did not result in formation o[ the cyclophane. Crystals of the cyclophane were monoclinic, P2,/n, a = 9.620(3), b = 12.266(3), c = 1 1.994(2), A, P = 1 1 1.25(2)", Z = 4. Intensities were measured with a Nicolet P3 diffractometer and MoKa radiation at room temperature. The structure was solved by direct methods and refined to R = 0.0683, R,,. = 0.0493 based on 1730 reflections. The molecule shows some strain, but bond lengths and angles are normal. Attempts to relieve the strain are made by a small distortion of tbe purine rings and bending of the N6 and C8' atoms out of the planes to which they are attached (0.314(4), 0.459(5) A). Further, the N6,H6,Clf group is twisted by 30" from the pyrimidine plane and the torsion angles in the aliphatic chain are distorted from the idealized 60, 120, 180" (average, 13.6"; range 5.1-24.9"). These distortions result in some weakening of the T-bonding in the adenine moiety.Key words: purinophane synthesis, nucleophilic aromatic substitution, conformational analysis, crystal structure. On a rkalise la synthkse du cyclophane N6,N9-octamCthylene purine et on dttern~inC sa structure par diffraction des rayons-X par un cristal unique. On a prepare ce cyclophane en utilisant la 6-chloropurine et I'acide 8-amino-octanoi'que comme produits de depart. On a d'abord relie la fragment amino-octyle a I'azote N9 de la 6-chloropurine 2 l'aide de la rCaction de Mitsunobu et on a ensuite effectuk la cyclisation en cyclophane en faisant appel a une attaque nuclCophile du groupe amin6 sur la position C6 qui provoque un dCplacement de I'ion chlorure. Lorsque la strategie des reactions est inversCe, il n'y a pas de formation de cy~lophane. Les cristaux du cyclophane sont monocliniques, P 2 , / n , avec LZ = 9,620(3), b = 12,266(3) et c = 11.994(2) A, P = 1 1 1,25(2)" et Z = 4. On a mesurC les intensit6 a l'aide d'un diffractomktre P3 de Nicolet et en utilisant la radiation MoKa, la temperature ambiante. On a rksolu la structure par des mCthodes directes et on l'a affinCe jusqu'i des valeurs de R = 0,683 et R,,. = 0,0493 pour 1730 reflexions. La molCcule presente des tensions, toutefois les longeurs des liaisons et les angles sont normaux. Une partie de la tension est CliminCe par une faible distorsion des n9yaux purines et un dCplacement des atomes N6 et C8' hbrs des plans auxquels ils sont attaches (0,314(4) et 0,459(5) A respectivement). De plus, le groupe N6,H6,C11 fait un angle de 30" avec le plan de la pyrimidine et les angles de torsions dans la chaine aliphatique sont dCformes par rapport aux va...

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

“…The strategy for the synthesis of [9](N6,9)-6-aminopurinophane, 9, is outlined in Scheme 1 and, while it follows the methodology developed for the construction of [8](N6,9)-6-aminopurinophane (8), a more direct approach has been devised. 1,9-Nonanediol, 4, and 6-chloropurine, 6, were the two starting fragments.…”

“…Because the two conformers were of unequal population, approximately 75% of the anti form 9n and 25% of the syn form 96 as subsequently assigned (see Fig. 2), it was possible to use the 2D 6 45.03), 6-octylaminopurine (C1 ' 6 40.72), and 6-chloro-N9-octylpurine (N-C1' 6 44.48) (9), and thence their attached pairs of protons defined. Use was then made of the 2D COSY experiment where each proton could be linked with its neighbours along the chain and allowed each carbon to be assigned.…”

“…the aliphatic bridge of the [9]-purinophane enough flexibility to permit rotation about the C6-N6 bond to take place.…”

“…The crystal structure of [8](N6,9)-6-aminopurinophane (9) shows there are appreciable strains present in the molecule, with the N6 and C8' atomg being moved out of the heteroaromatic plane by 0.314 A and 0.459 A. respectively, towards the methylene chain, and the five-and six-membered rings twisted with respect to each other by 5.45". In view of these distortions we have undertaken the synthesis of [9](N6,9)-6-aminopurinophane and report herein its synthesis, NMR spectroscopy, and X-ray crystal structure.…”

“…In view of these distortions we have undertaken the synthesis of [9](N6,9)-6-aminopurinophane and report herein its synthesis, NMR spectroscopy, and X-ray crystal structure.…”