On the description of reactions in solution

A formulation for diffusion-influenced reactions in solution is given in which reactive and translational contributions are separated, steady state rate-limiting step formulations are generalized to the dynamical case and the influence of different experimental initial conditions is isolated.     

Dynamic effects on reaction rates in a Michael addition catalyzed by chalcone isomerase. Beyond the frozen environment approach

We present a detailed microscopic study of the dynamics of the Michael addition reaction leading from 6'-deoxychalcone to the corresponding flavanone. The reaction dynamics are analyzed for both the uncatalyzed reaction in aqueous solution and the reaction catalyzed by Chalcone Isomerase. By means of rare event simulations of trajectories started at the transition state, we have computed the transmission coefficients, obtaining 0.76 +/- 0.04 and 0.87 +/- 0.03, in water and in the enzyme, respectively. According to these simulations, the Michael addition can be seen as a formation of a new intramolecular carbon-oxygen bond accompanied by a charge transfer essentially taking place from the nucleophilic oxygen to the carbon atom adjacent to the carbonyl group (C (alpha)). As for intermolecular interactions, we find a very significant difference in the evolving solvation pattern of the nucleophilic oxygen in water and in the enzyme. While in the former medium this atom suffers an important desolvation, the enzyme provides, through variations in the distances with some residues and water molecules, an essentially constant electric field on this atom along the reaction progress. Grote-Hynes (GH) theory provides a useful framework to systematically analyze all the couplings between the reaction coordinate and the remaining degrees of freedom. This theory provides transmission coefficients in excellent agreement with the Molecular Dynamics estimations. In contrast, neither the frozen environment approach nor Kramers theory gives results of similar quality, especially in the latter case, where the transmission coefficients are severely underestimated. The (unusual) failure of the frozen environment approach signals the importance of some dynamical motions. Within the context of GH theory, analysis of the friction spectrum obtained in the enzymatic environment, together with normal-mode analysis, is used to identify those motions, of both the substrate and the environment, strongly coupled to the reaction coordinate and to classify them as dynamically active or inactive.     

13C and 1H NMR analysis of the nitration products of 2-amino-4-oxo-(3H)-5-trifluoromethylquinazoline and 2-amino-4-oxo-(3H)-5-fluoroquinazoline

Nitration of 2-amino-4-oxo-(3H)-5-trifluoromethylquinazoline is shown to occur exclusively at C⁶ as determined from an analysis of long range ¹H and ¹⁹F scalar couplings to ring carbons. Nitration of 2-amino-4-oxo-(3H)-5-fluoroquinazoline is found to occur both at C⁶ and C⁸ as evident from an analysis of the ¹⁹F and ¹H couplings of the ring protons.     

A stochastic theory of chemical reaction rates. I. Formalism

A class of stochastic processes is studied that can be used to model elementary and complex chemical reactions composed of a series of several distinct steps. Formal correlation function expressions are directly computed for the stochastic model to yield the overall rate constant for the reaction. One of the main results is a formula connecting the overall rate constant to the rate constants characterizing the elementary steps of the reaction.     

N-Amination of pyrrole and indole heterocycles with monochloramine (NH2Cl)

A survey of several electrophilic ammonia reagents for the N-amination of indole- and pyrrole-containing heterocycles revealed that monochloramine (NH(2)Cl) is an excellent reagent for this transformation. Pyrroles and indoles containing a variety of substitution were aminated on nitrogen with isolated yields ranging from 45% to 97%.