Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg2+-sensitive dye

Abstract

A density-fragment interaction ͑DFI͒ approach for large-scale calculations is proposed. The DFI scheme describes electron density interaction between many quantum-mechanical ͑QM͒ fragments, which overcomes errors in electrostatic interactions with the fixed point-charge description in the conventional quantum-mechanical/molecular-mechanical ͑QM/MM͒ method. A self-consistent method, which is a mean-field treatment of the QM fragment interactions, was adopted to include equally the electron density interactions between the QM fragments. As a result, this method enables the evaluation of the polarization effects of the solvent and the protein surroundings. This method was combined with not only density functional theory ͑DFT͒ but also time-dependent DFT. In order to evaluate the solvent polarization effects in the DFI-QM/MM method, we have applied it to the excited states of the magnesium-sensitive dye, KMG-20. The DFI-QM/MM method succeeds in including solvent polarization effects and predicting accurately the spectral shift caused by Mg 2+ binding.

Chromophore-specific theoretical spectroscopy: From subsystem density functional theory to mode-specific vibrational spectroscopy

“…The divide-and-conquer strategy by Yang [18] partitions the electron density in real space into interacting subsystem contributions, but uses a Hilbert-space partitioning of the Kohn-Sham Hamiltonian in terms of localized basis sets to calculate the subsystem densities. Recently, a more approximate scheme was proposed that only considers the electrostatic interactions based on the fragment densities in the context of density-functional theory [19]. Yang's divide-and-conquer strategy has been transferred from the context of density-functional theory to Hartree-Fock [20], second-order Møller-Plesset (MP2) [21,22], and coupled cluster theory [23].…”

“…The Thomas-Fermi-von Weizsäcker functional T TFW from Eq. (19) was applied, in which the parameter λ was varied from 0 to 1. For λ = 2/3, a very good agreement of the difference in solvation free energies with experiment was obtained.…”

Subsystem‐Based Theoretical Spectroscopy of Biomolecules and Biomolecular Assemblies

“…[225] From the amino-acid sequence similarity, it appears that structural issues may be important for the difference between HR and HG on the one hand, and HB on the other hand. [225,230,245] But a final assessment of the spectral shifts in these proteins will probably not be possible without accurate crystal-structure information.…”

“…Several studies have addressed the color-tuning effects in other rhodopsins, for example, in bR and sRII [2,228,244] or in human red, green, and blue cone pigments, [225,231,245] where similar difficulties arise. The investigation of the latter pigments is further complicated by the fact that no experimental crystal structures, but only structures from homology modeling are available.…”

A DFT/TDDFT study of Li+ and Mg2+ interactions with ketocyanine dye

“…Recently the TDDFT methodology has been applied in studies of complexation-induced shifts in absorption or luminescence spectra of organic molecules, e.g. complexation of flavonoids with iron [14], complexation of organic dyes with Mg 2+ [15] or divalent metal ions [16].…”