Hydrogenation intramolecular nonbonding interactions

Adsorption alters the structure of an alkene, and the subsequent hydrogen transfers are accompanied by further changes in the organic moiety. The transition state for adsorption undoubtedly has greater double bond character than the transition state for the formation of the alkyl intermediate, which implies that intramolecular nonbonding interactions will be greater in the latter. 

There have appeared in the literature several reports on calculating probable H positions based on a consideration of intramolecular steric interactions between nonbonding atomsb. This method assumes that the geometry of the rest of the molecule (the non-hydrogen portion) is known. 

For many years, CDs were considered to have rigid truncated-cone structures although this concept was incompatible with the ease of their complex formation and several experimental findings (mainly obtained by NMR technique). Recent experimental results demonstrate that the complexes, held together by weak nonbonded interactions, must be flexible not only in solution but also in the solid state. The truncated-cone structure of HP-)3-CDs became more flexible since the intramolecular hydrogen bond is broken by the hydroxylpropyl substituent. This flexibility preferably explains the improvement of complex forming ability and dynamic character of the complexes of HP- -CDs [22]. 

We started our OFF analysis of hydrogen bonded crystals (Hagler, Huler and Lifson, 1974) about a decade ago, after we concluded a OFF analysis of intra- and intermolecular potentials for alkanes. The nonbonded interactions in the alkane force field were selected to be of the "n-6-1" type, namely composed additively from a Lennard-Jones ("n-6") potential, Eqs. (17) or (19), and a Coulomb ("1") potential (Eq. (21)). Atoms of the same molecule were considered as nonbonded if they were separated by at least 3 consecutive bonds. The Lennard-Jones (LJ) potential is commonly considered to be a "12-6" potential, that is, the exponent n in the repulsive term Ar is taken to be n = 12 (see above). Examining the LJ potential for alkanes, we found that the LJ parameters optimized for intramolecular interactions were too low for intermolecular interactions, while the LJ parameters optimized for intermolecular interactions were too high for intramolecular interactions. These trends -12... 

XIV n=6) are extremely low (0-5%) in either method. This is doubtless due to the severely increased steric interaction of nonbonded groups attached to the ring, i.e., an axial methyl group and three axial hydrogen atoms on either side of the ring, in addition to a lowering of the probability of intramolecular collision of the two reactive atoms at the chain ends. 

Intramolecular hydride transfer in equation 4 proceeds with an enzymelike EM of 6.5 X 106 M. In other words, the intramolecular reaction is 6.5 X 106 times faster than the intermolecular counterpart at 1 M concentration (11). Davis et al. (II) argued that relief of strain cannot explain the fast rate because (a) the equilibrium constant in equation 4 is close to unity and (b) force-field calculations show that hydroxy ketone is only 1.7 kcal/mol more strained than the corresponding diketone, which lacks nonbonded H/C=0 interactions. The extremely fast nucleophilic attack on the carbonyl is, however, expected from our spatiotemporal hypothesis. Because the mobile hydrogen is held rigidly only 2.35 A away from the carbonyl carbon, well under the suspected critical distance of 2.8 A (6), the conditions for an enzyme-like acceleration are met. 

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