Self-fulfilling cavitands: Packing alkyl chains into small spaces

Abstract

The present research was undertaken to determine the conformations of alkyl groups that are forced into small spaces. Unbranched alkyl groups assume fully extended conformations in the free space of solutions, because any bends in the structure create steric clashes between hydrogens along the chain. We synthesized a series of alkyl esters of a carboxylic acid attached to the inner surface of a vase-shaped container structure. The shorter esters (ethyl and propyl) can be accommodated in extended conformations, and even small solvent molecules can share the container's space. Longer (butyl-octyl) esters adopt increasingly coiled conformations that writhe rapidly in the limited space of the cavity. Even longer esters (nonyl and decyl) can be synthesized, but their containers become distorted, and their spectra indicate slowed internal motions of the alkyl groups within the space. In general, alkyl groups are readily contorted when their internal strains are compensated by attraction with the inner surfaces and the proper filling of space.coiled conformations ͉ self-assembly T he lowest energy conformation of normal alkanes is a fully extended (anti) one in solution, the gas phase, and the solid state. Each bend creates gauche interactions involving repulsion between hydrogens on the C i and C iϩ3 carbons, and each gauche configuration is associated with an increase in energy of Ϸ0.55 kcal͞mol in the liquid state (1). The small energy involved means that, for a given alkane, a number of conformers are typically present in equilibrium. For example, n-heptane has 13 different accessible conformers in rapid interconversion under ambient conditions (2).The recent literature describes several systems in which the energetic preference for the anti conformation may be overcome by imposing geometric constraints on the size and shape of the space available (3-11). Naturally occurring protein receptors (12) and synthetic host molecules contain binding cavities suitable for hydrocarbons, and a variety of conformations have been observed by crystallography in the former and NMR in the latter. Normal alkanes are simply flexible and adept at filling spaces of diverse shape. We have examined normal alkanes in several hosts: hexameric pyrogallolarene assemblies encompassing a roughly cube-like space of Ϸ1,300 Å 3 (11); vase-shaped, water-soluble cavitands having an open-ended pocket of Ϸ200 Å 3 (7, 8); and a cylindrical molecular capsule having an inner space of 425 Å 3 (6, 9). The behavior in these systems fits neither Fischer's (13) lock-and-key model nor the Thoma and Koshland (14) induced-fit model: the alkane contorts to be accommodated; it assumes the size, shape, and chemical surface that are proper to the space on offer in the receptor. For example, n-alkanes shorter than the cavity of the cylinder (Fig. 1) are bound in an extended conformation; if the alkanes are slightly too long, they adopt a compact helical conformation with several gauche configurations. This conformation is shorter and thicker: it allows the alkane t...

Hydroxyatrazine N -Ethylaminohydrolase (AtzB): an Amidohydrolase Superfamily Enzyme Catalyzing Deamination and Dechlorination

“…In addition, AtzB differentiates between straight-chained N-alkyls and N-alkyl ethers like N-propyl-3-methoxy side chains [2-hydroxy-4-(N-isopropylamino)-6-N-(3-methoxypropylamino)-1,3,5-triazine]. Purse and Rebek found that alkyl group conformational changes, such as anti to gauche transitions, occurred readily in response to space limitations (22). These transitions occur if the binding energy supplied by attractions to the container's inner surface compensates for any conformational energetics.…”

Slippage of a Porphyrin Macrocycle over Threads of Varying Bulkiness: Implications for the Mechanism of Threading Polymers through a Macrocyclic Ring

“…HRMS were measured on a JEOL JMS-T100CS AccuTOF. NMR spectra were taken on a Varian Inova 400 (400 MHz, 1 H and 2D spectra) instrument or on a Bruker DMX 300 (75 MHz, 13 C spectra) machine and were calibrated to an internal standard of tetramethylsilane (d = 0.00 ppm). Porphyrin macrocycle H 2 1 was synthesized according to a literature procedure.…”

“…The crude mixture was subjected to a flash silica column to obtain the corresponding primary alcohol. 2-Butylhexan-1-ol: [19b] Methylene solution: 10 (0.40 g, 2.9 mmol) in THF (30 mL); borane solution: 0.90 mL, 1.8 mmol; neutralization solutions: ethanol (6 mL), aqueous 3.0 m NaOH (35 mL) and aqueous 35 % H 2 O 2 (35 mL); eluent: n-pentane/diethyl ether, 9:1 (v/v); yield = 0.32 g as a colourless liquid (2.0 mmol, 69 %); 1 H NMR (400 MHz, CDCl 3 ): d = 3.54 (t, 2 H, HOCH 2 , J = 5.6 Hz), 1.45 (m, 1 H, HOCH 2 CH), 1.38-1.22 (m, 12 H, HOCH 2 -CHCH 2 CH 2 CH 2 ), 1.18 (t, 1 H, OH, J = 5.6 Hz), 0.90 ppm (t, 6 H, CH 3 , J = 7.2 Hz); 13 C NMR (75 MHz, CDCl 3 ): d = 65. 14, 40.00, 30.14, 28.62, 22.61, 13.57 ppm.…”

“…The resulting solid was mixed with 2 mL of acetone followed by the addition of an excess of NH 4 PF 6 (s) and the product was precipitated by the addition of water (10 mL). The precipitate was filtered, washed with water (40 mL) followed by Et 2 O (10 mL) and then dried to obtain V7 as a white solid in a yield of 306 mg (0.25 mmol, 73 %); .02 (t, 1 H, para-ArH, J = 1.6 Hz), 6.73 (d, 2 H, ortho-ArH, J = 1.6 Hz), 4.68 (t, 2 H, NCH 2 , J = 7.6 Hz), 4.51 (d, 2 H, NCH 2 , J = 7.6 Hz), 4.00 (t, 2 H, OCH 2 , J = 6 Hz), 2.11 (m, under water peak, 2 H, CH 2 ), 2.04 (m, under water peak, 1 H, CH), 1.86 (dd, 2 H, CH 2 , J = 7.2 Hz), 1.62 (dd, 2 H, CH 2 , J = 7.2 Hz), 1.45-1.15 (m, 64 H, CH 2 ), 1.30 (s, 18 H, CH 3 ), 0.88 ppm (t, 6 H, CH 3 , J = 6.8 Hz); 13 C NMR (75 MHz, CD 3 CN/CDCl 3 , 1:1 (v/v)): d = 158. 14, 151.73, 149.44, 149.29, 145.34, 145.13, 126.84, 126.74, 114.37, 108.31, 66.57, 65.45, 61.74, 39.54, 34.33, 31.31, 30.61, 29.54, 29.07, 28.11, 25.19, 22.08, 13.34 1-(Cyclododecylmethyl)-1'-[5- (3,5-di-tert-butylphenoxy)pentyl]-4,4'-bipyridine-1,1'-diium dihexafluorophosphate (V8): [7a] A 25 mL flask, closed with a septum, containing a solution of 2 (44 mg, 0.087 mmol) and~62 mg of 6 (0.092 mmol) in DMF (1 mL) (108 mg of the mixture containing 6 and the elimination product of 6) was stirred for 3 days at 95 8C.…”

Challenges and breakthroughs in recent research on self-assembly

“…For example, they reported an unusual hetero-guest inclusion by a hydrogen-bonded molecular capsule, with preferential accommodation of a molecule each of benzene and p-xylene [38]. Their self-assembled capsule also provides a medium for stabilization of reactive intermediates [39], to shift the equilibrium between two stereoisomers [40], or to regulate the conformation of a guest species [41]. They expanded their self-assembled cavitand capsules by the addition of appropriate spacers, permitting variation of guest selectivity, while also demonstrating attachment of a rotating door unit to the cavitands [42,43].…”