Hybrid QM/MM potentials of mean force with interpolated corrections

Article Abstract:

A simple but efficient way to obtain corrected quantum mechanics/molecular mechanics (QM/MM) potentials of mean force (MF) is developed and proposed for chemical processes in condensed media. The structures selected to evaluate the energy correction are chosen from a reaction path obtained in the condensed media, ensuring then that they are representative of the ensemble of structures sampled during the simulation.

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Catalytic mechanism of dihydrofolate enzyme. A combined quantum-mechanical/molecular-mechanical characterization of the N5 protonation step

Article Abstract:

A theoretical investigation is done of the protonation of N5 of the hydrofolate, the prior step of the hydride transfer in dihydrofolate reductase. Hybrid quantum-mechanical/molecular-mechanical (QM/MM) calculations involving a flexible active-site region are used in combination with GRACE software. The calculations reveal the active role of the water molecules that are detected in all DHFR crystal structures.

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A QM/MM study of the conformational equilibria in the chorismate mutase active site. The role of the enzymatic deformation energy contribution

Article Abstract:

A conformational structures search of chorismate mutase substrate is carried out using in vacuo AM1, and MP2/6-31G methods and by means of a hybrid quantum mechanical/molecular mechanical procedure in the solvated enzyme. These specific interactions between the substrate and the enzyme environment change the order of stability of the different conformers obtained in vacuo, thus stabilizing those structures.

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