A classical trajectory mapping method was developed to study chemical reactions in solution and in enzymes. In this method, the trajectories were calculated on a classical potential surface and the free energy profile was obtained by mapping the classical surface to the quantum mechanical surface ob
Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution
β Scribed by Haiyan Liu; Yunyu Shi
- Publisher
- John Wiley and Sons
- Year
- 1994
- Tongue
- English
- Weight
- 658 KB
- Volume
- 15
- Category
- Article
- ISSN
- 0192-8651
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β¦ Synopsis
The procedure of combined semiempirical quantum mechanical (AM11 and molecular mechanical potential7 was used to study the nucleophilic addition of hydroxide to formaldehyde in solution. The gas phase AM1 potential surface is approximately 26 kcal/mol more exothermic than the corresponding ab initio 6-31 + G* calculation results. The free energy profile for the reaction in solution was determined by means of molecular dynamic simulations. The resulting free energy of activation is approximately 5 kcal/mol. The difference of the free energy of solvation between the reactant and the product states is about 38 kcal/mol. As the reaction goes on, the number of hydrogen bonds formed by the hydroxide oxygen with the surrounding water molecules decreases, whereas the number of hydrogen bonds formed by the carbonyl oxygen increases. There is no significant change in the total number of hydrogen bonds between the solute and the solvent molecules, and the average number of these hydrogen bonds is between five and six during the entire reaction process. These results are consistent with previous studies using a model based on ad initio 6-31 + G* calculations in the gas phase. The reaction path in solution is different from the gas phase minimum energy reaction path. When the two reactants are at a large distance, the attack route of the hydroxide anion in solution is close to perpendicular to the formaldehyde plane, whereas in the gas phase the route is collinear with the carbonyl group. These results suggests that although AM1 does not yield accurate energies in the gas phase, valuable insights into the solvent effects can be obtained through computer simulations with this combined potential. This combined procedure could be applied to chemical reactions within macromolecules, in which a quantitative estimation of the effects of the environment would not be easily attainable by another technique.
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The errors made when large chemical systems are replaced by small models are discussed: interrupted charge transfer, missing structure constraints, neglected long-range interactions. A combined quantum mechanics (QM)-interatomic potential function (Pot) approach is described. Characteristic features
## Abstract In this study, we investigated the Cο£ΏH bond activation of methane catalyzed by the complex [PtCl~4~]^2β^, using the hybrid quantum mechanical/effective fragment potential (EFP) approach. We analyzed the structures, energetic properties, and reaction mechanism involved in the elementary