Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators - Aix-Marseille Université Accéder directement au contenu
Article Dans Une Revue Journal of Chemical Theory and Computation Année : 2024

Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators

Simone Bonfrate
Nicolas Ferré
Miquel Huix-Rotllant

Résumé

Long-range electrostatic effects are fundamental for describing chemical reactivity in the condensed phase. Here, we present the methodology of an efficient quantum mechanical/molecular mechanical (QM/MM) model in periodic boundary conditions (PBC) compatible with QM/MM boundaries at chemical bonds. The method combines electrostatic potential fitted charge operators and electrostatic potentials derived from the smooth particle-mesh Ewald (PME) sum approach. The total energy and its analytic first derivatives with respect to QM, MM, and lattice vectors allow QM/MM molecular dynamics (MD) in the most common thermodynamic ensembles. We demonstrate the robustness of the method by performing a QM/MM MD equilibration of methanol in water. We simulate the cis/trans isomerization free-energy profiles in water of proline amino acid and a proline-containing oligopeptide, showing a correct description of the reaction barrier. Our PBC-compatible QM/MM model can efficiently be used to study the chemical reactivity in the condensed phase and enzymatic catalysis.
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jeudi 7 novembre 2024
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0 3 11
Année Mois Jours
Avant la publication
jeudi 7 novembre 2024
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jeudi 7 novembre 2024
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Dates et versions

hal-04610504 , version 1 (13-06-2024)

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Simone Bonfrate, Nicolas Ferré, Miquel Huix-Rotllant. Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators. Journal of Chemical Theory and Computation, 2024, 20 (10), pp.4338-4349. ⟨10.1021/acs.jctc.4c00201⟩. ⟨hal-04610504⟩
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