Yue-Jie Ai

Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein

Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.

Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore.

We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.

X-ray spectroscopy of blocked alanine in water solution from supermolecular and supermolecular-continuum solvation models: a first-principles study

The N1s near-edge X-ray absorption fine structure (NEXAFS) and X-ray emission spectra (XES) of blocked alanine in water solution have been investigated at the first-principles level based on cluster models constructed from classical molecular dynamics simulations. The bulk solvent has been described by both supermolecular and combined supermolecular-continuum models. With the former model we show that NEXAFS spectra convergent with respect to system size require at least the inclusion of the second solvation shell and that averaged spectra over several hundreds of snapshots can well represent the statistical effect of different instantaneous configurations of the solvation shells. With the combined model we demonstrate that calculations of a medium-sized peptide-water supermolecule qualitatively predict the NEXAFS spectrum of the solvated peptide even considering a single geometry. Furthermore, sampling over hundreds of snapshots by the combined model, the explicit inclusion of even a few waters yields an averaged spectrum in good quantitative agreement with the discrete model results. In comparison, the XES spectra show little dependence on the structures of either the solvent shell or the peptide itself. The ramifications of these findings are discussed.

Conical intersection is responsible for the fluorescence disappearance below 365 nm in cyclopropanone.

The photodissociation dynamics of cyclopropanone was explored with the complete active space self-consistent field (CASSCF) calculations and ab initio nonadiabatic molecular dynamics simulations. The related minima, transition state (TS) and minimum-energy conical intersections (MECIs) were obtained as well as energetics. In the static CASSCF calculations, one MECI was found to be responsible for the fluorescence disappearance below 365 nm because the ultrafast internal conversion (IC) via this MECI deprived the opportunity of the fluorescence emission. Further evidence of this ultrafast IC event came from the subsequent ab initio nonadiabatic molecular dynamics simulations.

Ultrafast deactivation processes in the 2-aminopyridine dimer and the adenine-thymine base pair: similarities and differences.

2-Aminopyridine dimer has frequently been used as a model system for studying photochemistry of DNA base pairs. We examine here the relevance of 2-aminopyridine dimer for a Watson-Crick adenine-thymine base pair by studying UV-light induced photodynamics along two main hydrogen bridges after the excitation to the localized (1)pi pi(*) excited-state. The respective two-dimensional potential-energy surfaces have been determined by time-dependent density functional theory with Coulomb-attenuated hybrid exchange-correlation functional (CAM-B3LYP). Different mechanistic aspects of the deactivation pathway have been analyzed and compared in detail for both systems, while the related reaction rates have also be obtained from Monte Carlo kinetic simulations. The limitations of the 2-aminopyridine dimer as a model system for the adenine-thymine base pair are discussed.

Direct determination of resonance energy transfer in photolyase: structural alignment for the functional state.

Photoantenna is essential to energy transduction in photoinduced biological machinery. A photoenzyme, photolyase, has a light-harvesting pigment of methenyltetrahydrofolate (MTHF) that transfers its excitation energy to the catalytic flavin cofactor FADH¯ to enhance DNA-repair efficiency. Here we report our systematic characterization and direct determination of the ultrafast dynamics of resonance energy transfer from excited MTHF to three flavin redox states in E. coli photolyase by capturing the intermediates formed through the energy transfer and thus excluding the electron-transfer quenching pathway. We observed 170 ps for excitation energy transferring to the fully reduced hydroquinone FADH¯, 20 ps to the fully oxidized FAD, and 18 ps to the neutral semiquinone FADH•, and the corresponding orientation factors (κ2) were determined to be 2.84, 1.53 and 1.26, respectively, perfectly matching with our calculated theoretical values. Thus, under physiological conditions and over the course of evolution, photolyase has adopted the optimized orientation of its photopigment to efficiently convert solar energy for repair of damaged DNA.

Nonradiative decay of the lowest excited singlet state of 2-aminopyridine is considerably faster than the radiative decay

Ab initio calculations reveal that radiative lifetime of the lowest excited singlet state of 2-aminopyridine molecule should be around 20 ns, consistent with the molecules of the same type but is about one order of magnitude larger than the claimed experimental fluorescent lifetime in recent years. An S(1)/S(0) conical intersection close to the S(1) state has been located, which could be the possible nonradiative channel that is responsible for the fast decay observed in the experiment.

Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States

Intrinsic Property of Flavin Mononucleotide Controls its Optical Spectra in Three Redox States

Nonadiabatic histidine dissociation of hexacoordinate heme in neuroglobin protein.

In the present work, density functional theory and canonical nonadiabatic Monte Carlo transition state theory have been used to investigate the histidine dissociation process from hexacoordinate heme in Ngb protein. The potential energy surfaces (PES) of the lowest singlet, triplet, and quintet states are calculated by stepwise optimization along with the histidine dissociation pathway. Based on the calculated two-dimensional PES, the histidine dissociation rates for the spin-forbidden processes via singlet to triplet and singlet to quintet transitions have been calculated by the nonadiabatic Monte Carlo transition state theory in canonical ensemble. The present study provides a quantitative description on spin-forbidden histidine dissociation processes.