Ab Initio Quantum Mechanical and Molecular Dynamical Study of Intra- and Intermolecular Anhydride Formation

Transition state analogues for nucleotidyl transfer reactions: Structure and stability of pentavalent vanadate and phosphate ester dianions

The structures and energy of phosphate dimethyl ester and vanadate dimethyl ester have been calculated using B3LYP/TZVP density functional quantum chemical methods and polarized continuum (PCM) and Langevin dipoles solvation models. These calculations were carried out to obtain fundamental information on the ability of vanadate esters to function as transition state analogues for the nucleotidyl transfer reaction catalyzed by DNA polymerases. Base-catalyzed methanolysis of the phosphate and vanadate dimethyl esters were the model reactions examined in this study. The structures of the phosphate and vanadate dimethyl esters and pentavalent intermediates in aqueous solution were optimized and evaluated at the PCM/B3LYP/TZVP level. The three-dimensional free energy surfaces for the studied reactions were determined at the PCM/B3LYP/TZVP//B3LYP/TZVP level. Comparison with experimental structural data obtained from the Cambridge Structural Database and with the observed kinetics of phosphate diester hydrolysis demonstrated that the level of theory chosen for these studies was appropriate. The results showed that structurally and electrostatically the vanadate dimethylester and a five-coordinate nearly trigonal bipyramidal intermediate were reasonable analogues for the parent phosphorus systems. Despite these similarities in structure, the energetics of the two systems were different, and the transition states of the two model reactions were found on different areas of the potential energy surface. When the binding energy of a transition state-DNA polymerase complex was extrapolated to a transition state analogue-DNA polymerase complex, the formation of a simple dianionic pentavalent vanadate ester adduct in the enzyme active site was not found to be sufficiently favorable. This finding suggests that additional stabilization of this adduct is needed before this type of transition state analogue will be likely to yield stable adducts with this class of enzymes. New possible candidates for such complexes are suggested.

A phase-switch purification approach for the expedient removal of tagged reagents and scavengers following their application in organic synthesis

In this paper we wish to report on a variety of expedient chemical transformations and purifications achieved via a generic "catch and release" methodology, based on a synthetically inert bipyridyl chelating tag that can be selectively captured with a resin-bound copper(II) species. Utilising this approach we are able to derive many of the same benefits associated with both solid phase synthesis and supported reagent methods.

Site of nucleophilic attack and ring opening of five-membered heterocyclic 2,3-diones: a density functional theory study

The site of nucleophilic addition to five-membered heterocyclic 2,3-diones (4-iminomethylfuran-2,3-dione A1 and 4-formyl-pyrrole-2,3-dione B1) is studied by density functional theory calculations (B3LYP/6-31G) with water as the nucleophile. Both uncatalyzed and water-assisted 1,2-addition to the lactone (lactam) and the keto carbonyl group, and conjugate addition to C5 of the heterocycle and the heteroatom of the 4-iminomethyl (formyl) moiety are considered. In addition, concerted and stepwise ring fission of the lactone (lactam) ring is also treated. The effect of solvation (aqueous solution) is taken into account by the polarizable continuum model (PCM) and the Poisson-Boltzmann SCRF method (PB-SCRF), as well as explicit water molecules. Only this latter approach yields meaningful activation free energies. Barriers for addition of H2O increase in the order 1,4-addition to C5 < addition to the lactone (lactam) carbonyl < hydration of the 3-keto group. No reaction path for concerted water-assisted ring opening could be found.

Simulating enzyme reactions: challenges and perspectives

Elucidating how enzymes enhance the rates of the reactions that they catalyze is a major goal of contemporary biochemistry, and it is an area in which computational and theoretical techniques can make a major contribution. This article outlines some of the processes that need to be investigated if enzyme catalysis is to be understood, reviews the current state-of-the-art in enzyme simulation work, and highlights challenges for the future.