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.

Repair of DNA Dewar photoproduct to (6-4) photoproduct in (6-4) photolyase.

Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

Photorotamerization of matrix-isolated acrylic acid revisited.

In this study, the conformational preferences and photochemistry of acrylic acid (AA, CH(2)=CHCOOH) monomer isolated in cryogenic argon and krypton matrices were interpreted, based on results of quantum chemical calculations. Natural bond orbital analysis allowed to shed light on the main electronic effects determining the relative stability of the conformers of the molecule in the ground electronic state. The conformational isomerization taking place upon UV-irradiation of the matrix-isolated compound (λ ∼ 243 nm) was explained, based on theoretical complete active space self-consistent field/complete active space with second order perturbation theory (CASSCF/CASPT2) and time-dependent density functional theory (TD-DFT) results, allowing to rationalize the nearly equal populations of the two lowest energy conformers of the molecule observed in the photostationary state. Besides, details of the infrared spectra of the compound were reinterpreted based on the calculated spectra for the two most stable conformers of the molecule. In particular, the assignments for the out-of-plane A" symmetry vibrations were revised.

Theoretical studies on photoisomerizations of (6-4) and Dewar photolesions in DNA.

The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (CI) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S(2) ((1)ππ*) and the S(0) states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.

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.

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.

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.

How CO binds to hexacoordinated heme in neuroglobin protein.

In the present work, density functional theory (DFT) has been used to investigate CO binding to the hexacoordinated heme in neuroglobin (Ngb) protein. Structural relaxation of the selected model system in the protein environment has been fully included by the alternative quantum and molecular mechanical optimizations. The polarized continuum model (PCM) was used to simulate interaction between the model system and the protein environment. The CO binding could take place in a concerted way and a barrier of 17.9 kcal mol(-1) was predicted on the concerted singlet pathway, which is not favorable in energy. The adiabatically sequential pathway requires an energy of 14.5 kcal mol(-1) for formation of the singlet intermediate. There exist two nonadiabatic sequential pathways for the CO binding, which involves the triplet and quintet states of intermediate. Both the singlet/triplet and singlet/quintet intersections play an important role in nonadiabatic sequential processes, which enhance the probability that the processes occur. The nonadiabatic processes that involve the triplet and quintet states of intermediate are the most probable pathways for the CO binding to the hexacoordinated heme in Ngb to form the product complex.