Bimolecular Hydrogen-Bonding Interactions

Optimization of the Lennard-Jones parameters for the QM atoms (Eq. [4]) was accomplished at Buffalo in 1992 (Table 1). However, this was only possible with a compromise between the accuracy of the geometrical and energetic results of hydrogen-bonding interactions. i - ° In the FBK paper, it was noted that the hydrogen bond distances for certain interactions are longer than the ab initio results, whereas the interaction energies are too weak. We have noticed that the discrepancy becomes particularly severe when the QM 

Hgure 4 Illustration of bitnolecular complexes for acetic acid and cytosine with water 6-31G(d) values for the interaction energies (E) in kilocalories per mole, and distances in angstroms are followed by the AM1/TIP3P results (in parentheses), and OPLS results, respectively. Monomer geometries are fixed in the energy optimizations. The ab initio results for cytosine-water complexes are from Ref. 136. 

In this procedure, the electronic terms of the QM/MM interaction Hamiltonian for A and B are first annihilated, leaving only the Lennard-Jones terms, which are gradually mutated from structure A into structure B. The latter mutation consists of empirical potentials, while standard methods are employed for the conversion.Absolute free energies of solvation can also be determined following a procedure developed by Cieplak and Koll-man, in which A is made to vanish in solution  

A different implementation of the free energy perturbation method was introduced by Bash, Field, and Karplus, who used a linear coupling between the two molecular systems  

In this approach, the coexistence oi both solute molecules in the presence a common solvent environment is required. Applying the AMl(MNDO)/ CHARMM potential, the free energy of activation for the 5 2 reaction, Cl + CH3CI - CICH3 + Cl, was computed and found to be in good agreement with experiment and previous theoretical data. The method has been successfully used in classical molecular dynamics simulation of proteins in aqueous solution.1 8-151 

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One of the most important characteristics of micelles is their ability to enclose all kinds of substances. Capture of these compounds in micelles is generally driven by hydrophobic, electrostatic and hydrogen-bonding interactions. The dynamics of solubilization into micelles are similar to those observed for entrance and exit of individual surfactant molecules, but the micelle-bound substrate will experience a reaction environment different from bulk water, leading to kinetic medium effects308. Hence, micelles are able to catalyse or inhibit reactions. The catalytic effect on unimolecular reactions can be attributed exclusively to the local medium effect. For more complicated bimolecular or higher-order reactions, the rate of the reaction is affected by an additional parameter the local concentrations of the reacting species in or at the micelle. 

Retro-Diels-Alder reactions of anthracenedione (51a) have been shown to proceed faster in aqueous solution than in organic solvents, apparently as a consequence of enhanced hydrogen bonding of water to the activated complex,30 since hydrophobic interactions with (51a) are of negligible importance. The results have been compared with previous kinetic data for bimolecular and intramolecular Diels-Alder reactions and the corresponding hydrogen bond and hydrophobic interactions have been discussed. 

Grubbs WT, Dougherty TP, Heilweil EJ. Bimolecular interactions in (Et)3SiOH base CCl4 hydrogen-bonded solutions studied by deactivation of the free OH-stretch vibration. J Am Chem Soc 1995 117 11989-11992. 

Rebek and his co-workers have shown that replication - autocatalysis based on molecular recognition - best accommodates the facts observed in the reaction of 42 with 43, and that under the published conditions 44 is responsible for the autocatalysis. The results indicated template-catalyzed replication as the source of autocatalysis, where recognition surfaces and functional groups interact to form a productive termolecular complex. The mechanism demands that catalysis would be absent with esters that lack hydrogen-bonding sites. One complication of this system is that the initial product of this bimolecular preassociative mechanism is postulated to be a cw-amide, which isomerized to the frani-amide, the active form of template. This appears to be one major background reaction for product formation (Scheme 14). 

It is also well known that the keto-enol equilibrium is modified fundamentally in aqueous solution due to the specific interaction of solvent molecules with the substrates through hydrogen bonds Calculated results summarized in Figure 39a indicate that the keto-enol equilibrium is markedly modified in the bimolecular neutral systems in which each tautomer interacts with one water molecule. In particular, the energy barrier for hydrogen transfer from oxygen to carbon is reduced appreciably, in going from... 

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