Hydrogen bonding molecular mechanics

Mechanistic studies on this system have demonstrated that the reaction does not follow a simple stepwise condensation pathway as first assumed. Instead, the authors have proposed a divergent mechanism by which the production of 2 and 3 are linked by a common intermediate (see Scheme 3). In such a mechanism, hydrogen-bonding interactions between the donor molecular moieties and the templating halide (acceptor) play an important role. 

A review has illustrated the importance of atomic-level DFT studies in elucidation of the function of hydrogen bonds in organocatalytic reactions through influence on the mechanism of substrate activation and orientation, and the stabilization of transition states and intermediates. Examples discussed include stereoselective catalysis by bifunctional thioureas, solvent catalysis by fluorinated alcohols in epoxidation by hydrogen peroxide, and intra-molecular cooperative hydrogen bonding in trans-a,a -(dimethyl-l,3-dioxolane-4,5-diyl)bis(diphenyl methanol) (TADDOL) (7)-type catalysts. ... 

Absorption, metaboHsm, and biological activities of organic compounds are influenced by molecular interactions with asymmetric biomolecules. These interactions, which involve hydrophobic, electrostatic, inductive, dipole—dipole, hydrogen bonding, van der Waals forces, steric hindrance, and inclusion complex formation give rise to enantioselective differentiation (1,2). Within a series of similar stmctures, substantial differences in biological effects, molecular mechanism of action, distribution, or metaboHc events may be observed. Eor example, (R)-carvone [6485-40-1] (1) has the odor of spearrnint whereas (5)-carvone [2244-16-8] (2) has the odor of caraway (3,4). 

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