Quantum mechanical/molecular mechanical/continuum style solvation model: Second order Møller-Plesset perturbation theory

Abstract

A combined quantum mechanical/molecular mechanical/continuum (QM/MM/C) style second order Møller-Plesset perturbation theory (MP2) method that incorporates induced dipole polarizable force field and induced surface charge continuum solvation model is established. The Z-vector method is modified to include induced dipoles and induced surface charges to determine the MP2 response density matrix, which can be used to evaluate MP2 properties. In particular, analytic nuclear gradient is derived and implemented for this method. Using the Assisted Model Building with Energy Refinement induced dipole polarizable protein force field, the QM/MM/C style MP2 method is used to study the hydrogen bonding distances and strengths of the photoactive yellow protein chromopore in the wild type and the Glu46Gln mutant.

A Dynamic Equilibrium of Three Hydrogen-Bond Conformers Explains the NMR Spectrum of the Active Site of Photoactive Yellow Protein

“…While extensive experimental and theoretical investigations − to date were concentrated on the signaling state formation, the hydrogen bonding network involving the p CA chromophore in the inactive/dark-adapted state of PYP has been a matter of much debate and remains poorly understood. Numerous studies have dealt with the geometric arrangement of the hydrogen bond (HB) donors in PYP’s active site (shown schematically in Figure ), , namely the Glu46 and Tyr42 residues, as well as the strength and type of the HBs found between these residues and p CA. − The Glu46 proton in particular has been the subject of considerable debate, as the formation of a so-called low barrier hydrogen bond (LBHB) with p CA was proposed . This idea is motivated by the crystal structure obtained via neutron diffraction experiments where (i) a short O­(Glu46)-O­( p CA) distance of 2.56 Å was observed and (ii) the Arg52 residue was assigned as a neutral species .…”