Molecular dynamics simulation in aqueous solution of N -methylazetidinone as a model of β -lactam antibiotics

In this article, we analyze the results of a molecular dynamics simulation in aqueous solution of the N-methylazetidinone molecule, often used to model β-lactam antibiotics. The radial distribution functions (RDFs) corresponding to the most interesting atoms, in terms of reactivity, are presented. We focus our study on the effect of a polar environment on the molecule. The solvent structure around the system is compared to the structure of β-lactam-water complexes, as obtained in a previous study of reaction mechanisms for the neutral and alkaline hydrolyses of N-methylazetidinone. Two types of complexes have been considered which are related to different hydrolysis mechanisms having simila…

A quantum mechanics/molecular mechanics study of the acylation reaction of TEM1 β-lactamase and penicillanate

The acylation step in β-lactamase catalyzed hydrolysis of β-lactams has been explored by means of a quantum mechanics/molecular mechanics approach (AM1/CHARMM). The TEM1 enzyme, a class A β-lactamase, and the penicillanate constitute the system employed in our study. The entire molecular system is divided into a quantum and a classical region: the quantum part is composed by the substrate, the serine Ser70 and the essential moieties of key active site residues, Lys73, Ser130 and Glu166, as well as a water molecule present in the active site region, while the classical part is formed by the remaining residues and structural waters of the enzyme. In particular, the sequence of steps proposed …

Can hydrophobic interactions be correctly reproduced by the continuum models?

The ability of the continuum models to describe hydrophobic interactions is investigated. In this work we have studied the interactions between two methane molecules in aqueous solution by means of a continuum model. The resulting potential of mean force is in good agreement with those obtained using Monte Carlo and molecular dynamics techniques. The three energy contributions appearing in the continuum energy partition (electrostatic, dispersion−repulsion, and cavitation) have been analyzed. The cavitation free energy plays the most important role of the three, determining the existence of an energy barrier between the contact minimum and the separated methane monomers. This barrier, which…

Modeling ?-lactam interactions in aqueous solution through combined quantum mechanics-molecular mechanics methods

Correction of cavity-induced errors in polarization charges of continuum solvation models