Fragment molecular orbital calculations for excitation energies of blue- and yellow-fluorescent proteins

Revisiting the Charge-Transfer States at Pentacene/C60 Interfaces with the GW/Bethe-Salpeter Equation Approach

Molecular orientations and interfacial morphologies have critical effects on the electronic states of donor/acceptor interfaces and thus on the performance of organic photovoltaic devices. In this study, we explore the energy levels and charge-transfer states at the organic donor/acceptor interfaces on the basis of the fragment-based GW and Bethe-Salpeter equation approach. The face-on and edge-on orientations of pentacene/C60 bilayer heterojunctions have employed as model systems. GW+Bethe-Salpeter equation calculations were performed for the local interface structures in the face-on and edge-on bilayer heterojunctions, which contain approximately 2000 atoms. Calculated energy levels and charge-transfer state absorption spectra are in reasonable agreements with those obtained from experimental measurements. We found that the dependence of the energy levels on interfacial morphology is predominantly determined by the electrostatic contribution of polarization energy, while the effects of induction contribution in the edge-on interface are similar to those in the face-on. Moreover, the delocalized charge-transfer states contribute to the main absorption peak in the edge-on interface, while the face-on interface features relatively localized charge-transfer states in the main absorption peak. The impact of the interfacial morphologies on the polarization and charge delocalization effects is analyzed in detail.

Emission shaping in fluorescent proteins: role of electrostatics and π-stacking

We obtained the fluorescence spectrum of the GFP with trajectory simulations, and revealed the role of the protein sidechains in emission shifts.

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

Spectral "Fine" Tuning in Fluorescent Proteins: The Case of the GFP-Like Chromophore in the Anionic Protonation State

Fluorescent proteins (FPs), featuring the same chromophore but different chromophore-protein interactions, display remarkable spectral variations even when the same chromophore protonation state, i.e. the anionic state, is involved. We examine the mechanisms behind this tuning by means of structural analysis, molecular dynamics simulations, and vertical excitation energy calculations using QM/MM Time-Dependent Density Functional Theory (TD-DFT), CASPT2/CASSCF, and SAC-CI. The proteins under investigation include the structurally similar, though spectrally distinct, Dronpa and mTFP0.7, with absorption peaks at 453 and 503 nm, respectively. We extend our analysis to two Green Fluorescent Protein variants, GFP-S65T (absorption peak at 484 nm), for comparison with previous computational studies, and GFP-S65G/V68L/S72A/T203Y, a yellow fluorescent protein (514 nm), in order to include one of the most red-shifted FPs containing a GFP-like chromophore. We compare different choices of the QM system, and we discuss how molecular dynamics simulations affect the calculation of excitation energies, with respect to X-ray structures. We are able to partially reproduce the spectral tuning of the FPs and correlate it to the chromophore bond-length variations, as determined by specific interactions with the chromophore environment.