Statistical Mechanical Modeling of Chemical Reactions in Complex Systems:  The Reaction Free Energy Surface

Amadei, Andrea; D’Alessandro, Maira; Aschi, Massimiliano

doi:10.1021/jp048788l

Cited by 44 publications

(75 citation statements)

References 19 publications

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“…2,3,15,17,21 In this section we describe more thoroughly the basic derivations and physical implications of PMM, extending its theoretical framework to model excitonic effects in multichromophore systems. Finally, we show how to use statistical analysis of PMM results in the electronic state space in order to characterize the nature of QC perturbed quantum states.…”

Section: Theorymentioning

confidence: 99%

Theoretical characterization of electronic states in interacting chemical systems

Amadei

D’Alessandro

D’Abramo

et al. 2009

The Journal of Chemical Physics

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In this article we characterize, by means of the perturbed matrix method, the response of the electronic states of a chemical system to the perturbing environment. In the theory section we describe in detail the basic derivations and implications of the method, extending its theoretical framework to treat possible excitonic effects, and we show how to characterize the perturbed electronic states. Finally, by using a set of chemical systems interacting with complex atomic-molecular environments, we describe the nature and general features of the electronic state mixing and transitions as caused by atomic and molecular interactions.

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Section: Theorymentioning

confidence: 99%

Theoretical characterization of electronic states in interacting chemical systems

Amadei

D’Alessandro

D’Abramo

et al. 2009

The Journal of Chemical Physics

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“…In this respect, we consider the repertoire of the electrostatic perturbation produced by the micelle and the solvent on the QC along the MD simulation, as statistically significant for all species along the reaction coordinate. 26,27 To summarize, as a consequence of these assumptions, 27 we can obtain the free energy barrier for the intracluster proton transfer by introducing a perturbation of the fluctuating micelle and solvent over the corresponding gas-phase reaction path (by means of PMM) using a single MD simulation ensemble.…”

Section: ' Introductionmentioning

confidence: 99%

Modeling of Chemical Reactions in Micelle: Water-Mediated Keto–Enol Interconversion As a Case Study

et al. 2011

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The effect of a zwitterionic micelle environment on the efficiency of the keto-enol interconversion of 2-phenylacetylthiophene has been investigated by means of a joint application of experimental and theoretical/computational approaches. Results have revealed a reduction of the reaction rate constant if compared with bulk water essentially because of the different solvation conditions experienced by the reactant species, including water molecules, in the micelle environment. The slight inhibiting effect due to the application of a static electric field has also been theoretically investigated and presented.

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“…[27][28][29][30] In this respect the main aim of this work is to introduce (and evaluate the reliability of) an alternative theoretical approach providing a tool, complementary to existing computational schemes, for addressing chemical reactions in solution. As a matter of fact in this paper we evaluate the reaction free energy surface of the reaction I in water, by means of a theoretical model based on statistical mechanics and the perturbed matrix method (PMM), [31][32][33][34][35][36][37] as introduced 38 and applied 39 in very recent papers. Moreover, using the quasi Gaussian entropy (QGE) theory 40 to model the reaction free energy in temperature, we are able to construct a complete theoretical description of the reaction thermodynamics.…”

Section: Introductionmentioning

confidence: 99%

Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde

Aschi

D’Abramo

Ramondo

et al. 2006

J of Physical Organic Chem

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The free energy profile and the (classical) kinetics of chemical reactions in (soft) condensed phase are modeled theoretically by means of molecular dynamics simulations, the Perturbed Matrix Method (PMM) and the quasi Gaussian entropy (QGE) theory. In this paper we describe the theoretical framework and apply the model to the intramolecular proton transfer reaction of aqueous malonaldehyde. Although in the present application we disregard the quantum effects for the proton dynamics along the reaction coordinate (i.e., tunneling), the classical-like view of the proton transition over the reaction free energy surface seems to properly describe the kinetic process and shows that water acts lowering the reaction free energy barrier. Moreover, a weak temperature dependence of the free energy surface is obtained, implying small entropy variations in the transition. Interestingly the activation entropy, as provided by the QGE model, is negative in the whole temperature range considered, thus indicating an entropy reduction at the transition structure. Finally, by comparing our results with theoretical and experimental literature data, we critically address the actual role of tunneling in this reaction and discuss the emerging kinetic scheme.

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Statistical Mechanical Modeling of Chemical Reactions in Complex Systems: The Reaction Free Energy Surface

Cited by 44 publications

References 19 publications

Theoretical characterization of electronic states in interacting chemical systems

Theoretical characterization of electronic states in interacting chemical systems

Modeling of Chemical Reactions in Micelle: Water-Mediated Keto–Enol Interconversion As a Case Study

Theoretical modeling of chemical reactions in complex environments: the intramolecular proton transfer in aqueous malonaldehyde

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