硫代乙酰胺光化学反应机理的理论研究

用B3LYP, MP2和CASSCF方法, 采用cc-pVDZ和6-31++G**基组, 研究了硫代乙酰胺在基态和最低三态上消除硫化氢以及其它光解离反应, 并考虑了单个溶剂分子参与反应对质子迁移反应的影响, 得到了消除硫化氢反应的反应机理, 计算结果可以很好地解释实验结果. 进而用CASSCF方法计算了第一激发单态上的各驻点, 以及各交叉点. 计算结果表明, 在S1和T1态上发生除分子内转动以外的化学反应的可能性比较小, 当分子被激发到S2态上时, 将通过S2/S1交叉点到S1态, 在S1态上的分子有两条途径去活化, 通过S1/S0交叉点到热基态, 通过S1/T1交叉点系间窜越到T1态. 因而得出CH3CSNH2发生光解离反应的可能性不大. 基于此, 可将硫代酰胺结构引入蛋白或多肽中, 有望在不破坏分子整体结构的情况下对其进行光化学研究.     

Theoretical study of proton coupled electron transfer reaction in the light state of the AppA BLUF photoreceptor

The BLUF (blue light sensor using flavin adenine dinucleotide) domain is widely studied as a prototype for proton coupled electron transfer (PCET) reactions in biological systems. In this work, the photo-induced concerted PCET reaction from the light state of the AppA BLUF domain is investigated. To model the simultaneous transfer of two protons in the reaction, two-dimensional potential energy surfaces for the double proton transfer are first calculated for the locally excited and charge transfer states, which are then used to obtain the vibrational wave function overlaps and the vibrational energy levels. Contributions to the PCET rate constant from each pair of vibronic states are then analyzed using the theory based on the Fermi's golden rule. We show that, the recently proposed light state structure of the BLUF domain with a tautomerized Gln63 residue is consistent with the concerted transfer of one electron and two protons. It is also found that, thermal fluctuations of the protein structure, especially the proton donor-acceptor distances, play an important role in determining the PCET reaction rate. © 2018 Wiley Periodicals, Inc.     

Directed Electron Transfer in Flavin Peptides with Oligoproline-Type Helical Conformation as Models for Flavin-Functional Proteins

To mimic the charge separation in functional proteins we studied flavin-modified peptides as models. They were synthesized as oligoprolines that typically form a polyproline type-II helix, because this secondary structure supports the electron transfer properties. We placed the flavin as photoexcitable chromophore and electron acceptor at the N-terminus. Tryptophans were placed as electron donors to direct the electron transfer over 0–3 intervening prolines. Spectroscopic studies revealed competitive photophysical pathways. The reference peptide without tryptophan shows dominant non-specific ET dynamics, leading to an ion pair formation, whereas peptides with tryptophans have weak non-specific ET and intensified directed electron transfer. By different excitation wavelengths, we can conclude that the corresponding ion pair state of flavin within the peptide environment has to be energetically located between the S₁ and S₄ states, whereas the directed electron transfer to tryptophan occurs directly from the S₁ state. These photochemical results have fundamental significance for proteins with flavin as redoxactive cofactor.     

Light-generated paramagnetic intermediates in BLUF domains

Blue-light sensitive photoreceptory BLUF domains are flavoproteins, which regulate various, mostly stress-related processes in bacteria and eukaryotes. The photoreactivity of the flavin adenine dinucleotide (FAD) cofactor in three BLUF domains from Rhodobacter sphaeroides, Synechocystis sp. PCC 6803 and Escherichia coli have been studied at low temperature using time-resolved electron paramagnetic resonance. Photoinduced flavin triplet states and radical-pair species have been detected on a microsecond time scale. Differences in the electronic structures of the FAD cofactors as reflected by altered zero-field splitting parameters of the triplet states could be correlated with changes in the amino-acid composition of the various BLUF domains' cofactor binding pockets. For the generation of the light-induced, spin-correlated radical-pair species in the BLUF domain from Synechocystis sp. PCC 6803, a tyrosine residue near the flavin's isoalloxazine moiety plays a critical role.     

HSO自由基电子基态激发态的CAS计算研究

使用CASSCF方法和ANO-L基组优化了HSO自由基的基态和3个低占据激发态的结构, 并采用包括更多电子动态相关能的CASPT2方法进行了单点能校正. 频率计算结果表明, 优化的4个几何为势能面上的稳定点. 通过电子结构的研究合理地解释了各个激发态相对于电子基态的结构变化.     

A CASSCF-CASPT2 study of the excited-state intramolecular proton transfer reaction in 1-amino-3-propenal using different active spaces

In this work we analyze how the choice of the active space in the CASSCF (the complete-active-space multiconfiguration self-consistent-field method) and CASPT2 (the second-order perturbation theory based on the CASSCF reference wave function) calculations affects the computed potential energy curves (PECs) for the intramolecular proton transfer reaction in the ground state and the two lowest lying singlet excited states of 1-amino-3-propenal. As anticipated, the results revealed that, qualitatively, the proton transfer in the different states can be correctly described even by minimal active spaces, which include the orbitals involved in the electronic excitation of the considered state and the antibonding sigma orbital corresponding to the bond formed by the molecule with the migrating hydrogen atom. However, quantitatively, the relative energies of the two tautomers and the energy barriers computed at the CASSCF level change when the active space is increased, indicating importance of the dynamic electron correlation. Introducing the dynamic correlation effects via CASPT2 makes the calculated energy parameters more uniform among the different active spaces. The analysis suggested certain optimal active spaces for studying proton transfer reactions in systems similar to 1-amino-3-propenal. The PEC calculations for excited states showed that the results are sensitive to the molecular geometries used in the calculations, particularly near the transition point. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1422–1431 (1999)     

Orientation of a key glutamine residue in the BLUF domain from AppA revealed by mutagenesis, spectroscopy, and quantum chemical calculations

The flavin-adenine-dinucleotide-binding BLUF domain constitutes a new class of blue-light receptors, and the N-terminal domain of AppA is a representative of this family. A crystal structure of the BLUF domain from AppA suggested that a conserved Gln63 forms a hydrogen bond with the flavin N5 atom. Upon light excitation, this residue is proposed to undergo a approximately 180 degrees rotation that leads to a rearrangement of a hydrogen bonding network. However, crystallographic studies on the other BLUF proteins claimed an opposite orientation for the glutamine residue. In this communication, we have revealed the presence of a Gln63-to-N5 hydrogen bond in the dark state of AppA by a combined approach of mutagenesis, spectroscopy, and quantum chemical calculations. The present finding supports the view that the reorientation of the Gln63 side chain is a key event in the signaling state formation of BLUF proteins.     

Enhanced intersystem crossing via a high energy charge transfer state in a perylenediimide-perylenemonoimide dyad

The electronic relaxation processes of a photoexcited linear perylenediimide-perylenemonoimide (PDI-PMI) acceptor-donor dyad were studied. PDI-PMI serves as a model compound for donor-acceptor systems in photovoltaic devices and has been designed to have a high-energy PDI (-*)-PMI (+*) charge transfer (CT) state. Our study focuses on the minimal Gibbs free energy (Delta G ET) required to achieve quantitative CT and on establishing the role of charge recombination to a triplet state. We used time-resolved photoluminescence and picosecond photoinduced absorption (PIA) to investigate excited singlet (S 1) and CT states and complemented these experiments with singlet oxygen ( (1)Delta g) luminescence and PIA measurements on longer timescales to study the population of triplet excited states (T 1). In an apolar solvent like cyclohexene (CHX), photoinduced electron transfer does not occur, but in more polar solvents such as toluene (TOL) and chlorobenzene (CB), photoexcitation is followed by a fast electron transfer, populating the PDI (-*)-PMI (+*) CT state. We extract rate constants for electron transfer (ET; S 1-->CT), back electron transfer (BET; S 1<--CT), and charge recombination (CR) to lower-energy states (CT-->S 0 and CT-->T 1). Temperature-dependent measurements yield the barriers for the transfer reactions. For ET and BET, these correspond to predictions from Marcus-Jortner theory and show that efficient, near quantitative electron transfer ( k ET/ k BET >or= 100) can be obtained when Delta G ET approximately -120 meV. With respect to triplet state formation, we find a relatively low triplet quantum yield (Phi T < 25%) in CHX but much higher values (Phi T = 30-98%) in TOL and CB. We identify the PDI (-*)-PMI (+*) state as a precursor to the T 1 state. Recombination to T 1, rather than to the ground-state S 0, is required to rationalize the experimental barrier for CR. Finally, we discuss the relevance of these results for electron donor-acceptor films in photovoltaic devices.     

Computational characterization of reaction intermediates in the photocycle of the sensory domain of the AppA blue light photoreceptor

The AppA protein with the BLUF (blue light using flavin adenine dinucleotide) domain is a blue light photoreceptor that cycle between dark-adapted and light-induced functional states. We characterized possible reaction intermediates in the photocycle of AppA BLUF. Molecular dynamics (MD), quantum chemical and quantum mechanical-molecular mechanical (QM/MM) calculations were carried out to describe several stable structures of a molecular system modeling the protein. The coordinates of heavy atoms from the crystal structure (PDB code 2IYG) of the protein in the dark state served as starting point for 10 ns MD simulations. Representative MD frames were used in QM(B3LYP/cc-pVDZ)/MM(AMBER) calculations to locate minimum energy configurations of the model system. Vertical electronic excitation energies were estimated for the molecular clusters comprising the quantum subsystems of the QM/MM optimized structures using the SOS-CIS(D) quantum chemistry method. Computational results support the occurrence of photoreaction intermediates that are characterized by spectral absorption bands between those of the dark and light states. They agree with crystal structures of reaction intermediates (PDB code 2IYI) observed in the AppA BLUF domain. Transformations of the Gln63 side chain stimulated by photo-excitation and performed with the assistance of the chromophore and the Met106 side chain are responsible for these intermediates.     

Why BLUF photoreceptors with roseoflavin cofactors lose their biological functionality

The photophysics of roseoflavin in three different environments is investigated by using ab initio and quantum mechanics/molecular mechanics methods. Intramolecular charge transfer is shown to be responsible for the quenching of the fluorescence in the gas phase, and in the water environment. However, for the roseoflavin incorporated into the blue light using flavin (BLUF) protein environment (substituting the native flavin) no such deactivation is found. The conical intersection between the locally excited state of the chromophore and the charge transfer state involving the tyrosine residue, which in the native BLUF domain is responsible for initiating the photocycle, is missing for the roseoflavin substituted protein. This explains the experimental observations of the lack of any photocycle, and the loss of the biological function of the BLUF photoreceptor reported earlier.     

Light-induced flipping of a conserved glutamine sidechain and its orientation in the AppA BLUF domain

The AppA BLUF domain is a blue light photoreceptor containing flavin. Conserved glutamine 63 is necessary for the photocycle of the protein, and its side chain has been proposed to flip in response to blue light illumination. Recently published crystal structures of AppA WT and the AppA mutant C20S describe contradictory conclusions regarding the orientation of the conserved glutamine 63 side chain in the dark. Here, we present evidence from NMR spectroscopy confirming light-induced flipping of the glutamine side chain to form a strong hydrogen bond between the glutamine 63 side chain carbonyl group and the tyrosine 21 side chain hydroxyl proton in the light-induced state. Our conclusions are consistent with published data from UV/vis absorbance and FTIR spectroscopy, as well as the crystal structure of AppA WT.     

Nonadiabatic dynamics of uracil: population split among different decay mechanisms

Nonadiabatic dynamics simulations performed at the state-averaged CASSCF method are reported for uracil. Supporting calculations on stationary points and minima on the crossing seams have been performed at the MR-CISD and CASPT2 levels. The dominant mechanism is characterized by relaxation into the S(2) minimum of ππ* character followed by the relaxation to the S(1) minimum of nπ* character. This mechanism contributes to the slower relaxation with a decay constant larger than 1.5 ps, in good agreement with the long time constants experimentally observed. A minor fraction of trajectories decay to the ground state with a time constant of about 0.7 ps, which should be compared to the experimentally observed short constant. The major part of trajectories decaying with this time constant follows the ππ* channel and hops to the ground state via an ethylenic conical intersection. A contribution of the relaxation proceeding via a ring-opening conical intersection was also observed. The existence of these two latter channels together with a reduced long time constant is responsible for a significantly shorter lifetime of uracil compared to that of thymine.     

A conclusive mechanism of the photoinduced reaction cascade in blue light using flavin photoreceptors

On the basis of extensive first-principle calculations within the framework of quantum mechanics/molecular mechanics (QM/MM), a conclusive mechanism for the formation of the signaling state of blue light using flavin (BLUF) domain proteins is proposed which is compatible with the experimental data presently available. Time-dependent density functional, as well as advanced coupled cluster response theory was employed for the QM part in order to describe the relevant excited states. One of the key residues involved in the mechanism is the glutamine adjacent to the flavin chromophore. The reaction cascade, triggered by the initial photoexcitation of the flavin chromophore, involves isomerization of this residue but no rotation as assumed previously. The fact that only the environment, but not the flavin chromophore by itself, is chemically transformed along the individual steps of the mechanism is unique for biological photoreceptors. The final isomer of the glutamine tautomer, i.e., the imidic acid, is further stabilized by the interchange of a methionine residue in the binding pocket with a tryptophan residue. The flip of these two residues might be the trigger for the large conformational change of this protein which is consequently transmitted as the signal to the biological environment.     

Excited-state properties and environmental effects for protonated schiff bases: a theoretical study.

Complete active space self-consistent field (CASSCF), multireference configuration interaction (MRCI), density functional theory (DFT), time dependent DFT (TDDFT) and the singles and doubles coupled-cluster (CC2) methodologies have been used to study the ground state and excited states of protonated and neutral Schiff bases (PSB and SB) as models for the retinal chromophore. Systems with two to four conjugated double bonds are investigated. Geometry relaxation effects are studied in the excited pipi* state using the aforementioned methods. Taking the MRCI results as reference we find that CASSCF results are quite reliable even though overshooting of geometry changes is observed. TDDFT does not reproduce bond alternation well in the pipi* state. CC2 takes an intermediate position. Environmental effects due to solvent or protein surroundings have been studied in the excited states of the PSBs and SBs using a water molecule and solvated formate as model cases. Particular emphasis is given to the proton transfer process from the PSB to its solvent partner in the excited state. It is found that its feasibility is significantly enhanced in the excited state as compared to the ground state, which means that a proton transfer could be initiated already at an early step in the photodynamics of PSBs.     

Distinguishing between relaxation pathways by combining dissociative ionization pump probe spectroscopy and ab initio calculations: a case study of cytosine

We present a general method for tracking molecular relaxation along different pathways from an excited state down to the ground state. We follow the excited state dynamics of cytosine pumped near the S(0)-S(1) resonance using ultrafast laser pulses in the deep ultraviolet and probed with strong field near infrared pulses which ionize and dissociate the molecules. The fragment ions are detected via time of flight mass spectroscopy as a function of pump probe delay and probe pulse intensity. Our measurements reveal that different molecular fragments show different timescales, indicating that there are multiple relaxation pathways down to the ground state. We interpret our measurements with the help of ab initio electronic structure calculations of both the neutral molecule and the molecular cation for different conformations en route to relaxation back down to the ground state. Our measurements and calculations show passage through two seams of conical intersections between ground and excited states and demonstrate the ability of dissociative ionization pump probe measurements in conjunction with ab initio electronic structure calculations to track molecular relaxation through multiple pathways.     

An ab initio study toward understanding the mechanistic photochemistry of acetamide

The potential energy surfaces for CH(3)CONH(2) dissociation into CH(3) + CONH(2), CH(3)CO + NH(2), CH(3)CN + H(2)O, and CH(3)NH(2) + CO in the ground and lowest triplet states have been mapped with DFT, MP2, and CASSCF methods with the cc-pVDZ and cc-pVTZ basis sets, while the S(1) potential energy surfaces for these reactions were determined by the CASSCF/cc-pVDZ optimizations followed by CASSCF/MRSDCI single-point calculations. The reaction pathways leading to different photoproducts are characterized on the basis of the computed potential energy surfaces and surface crossing points. A comparison of the reactivity among HCONH(2), CH(3)CONH(2), and CH(3)CONHCH(3) has been made, which provides some new insights into the mechanism of the ultraviolet photodissociation of small amides.     

Unraveling the flavin-catalyzed photooxidation of benzylic alcohol with transient absorption spectroscopy from sub-pico- to microseconds

Flavin-mediated photooxidations have been described for applications in synthetic organic chemistry for some time and are claimed to be a route to the use of solar energy. We present a detailed investigation of the involved photophysical and photochemical steps in methoxybenzyl alcohol oxidation on a timescale ranging from sub-picoseconds to tens of microseconds. The results establish the flavin triplet state as the key intermediate for the photooxidation. The initial step is an electron transfer from the alcohol to the triplet state of the flavin catalyst with (3)k(ET)≈ 2 × 10(7) M(-1) s(-1), followed by a proton transfer in ～6 μs. In contrast, the electron transfer involving the singlet state of flavin is a loss channel. It is followed by rapid charge recombination (τ = 50 ps) without significant product formation as seen when flavin is dissolved in pure benzylic alcohol. In dilute acetonitrile/water solutions of flavin and alcohol the electron transfer is mostly controlled by diffusion, though at high substrate concentrations >100 mM we also find a considerable contribution from preassociated flavin-alcohol-aggregates. The model including a productive triplet channel and a competing singlet loss channel is confirmed by the course of the photooxidation quantum yield as a function of substrate concentration: We find a maximum quantum yield of 3% at 25 mM of benzylic alcohol and significantly smaller values for both higher and lower alcohol concentrations. The observations indicate the importance to perform flavin photooxidations at optimized substrate concentrations to achieve high quantum efficiencies and provide directions for the design of flavin photocatalysts with improved performance.     

Sampling the proton transfer reaction coordinate in mixed quantum-classical molecular dynamics simulations

An umbrella sampling approach based on the vibrational energy gap is presented and examined for exploring the reaction coordinate for a proton transfer (PT) reaction. The technique exploits the fact that for a PT reaction the energy gap between the vibrational ground and excited states of the transferring proton reaches a minimum at the transition state. Umbrella sampling is used within mixed quantum-classical simulations to identify the transition state configurations and explore the reaction free energy curve and vibrationally nonadiabatic coupling. The method is illustrated by application to a model phenol-amine proton transfer reaction complex in a nanoconfined solvent. The results from this new umbrella sampling approach are consistent with those obtained from previous umbrella sampling calculations based on a collective solvent coordinate. This sampling approach further provides insight into the vibrationally nonadiabatic coupling for the proton transfer reaction and has potential for simulating vibrational spectra of PT reaction complexes in solution.     

Conical intersections in thymine

The mechanisms which are responsible for the radiationless deactivation of the npi* and pipi* excited singlet states of thymine have been investigated with multireference ab initio methods (the complete-active-space self-consistent-field (CASSCF) method and second-order perturbation theory with respect to the CASSCF reference (CASPT2)) as well as with the CC2 (approximated singles and doubles coupled-cluster) method. The vertical excitation energies, the equilibrium geometries of the 1npi*and 1pipi* states, as well as their adiabatic excitation energies have been determined. Three conical intersections of the S1 and S0 energy surfaces have been located. The energy profiles of the excited states and the ground state have been calculated with the CASSCF method along straight-line reaction paths leading from the ground-state equilibrium geometry to the conical intersections. All three conical intersections are characterized by strongly out-of-plane distorted geometries. The lowest-energy conical intersection (CI1) arises from a crossing of the lowest 1pipi* state with the electronic ground state. It is found to be accessible in a barrierless manner from the minimum of the 1pipi* state, providing a direct and fast pathway for the quenching of the population of the lowest optically allowed excited states of thymine. This result explains the complete diffuseness of the absorption spectrum of thymine in supersonic jets. The lowest vibronic levels of the optically nearly dark 1npi* state are predicted to lie below CI1, explaining the experimental observation of a long-lived population of dark excited states in gas-phase thymine.     

Modeling thymine photodimerizations in DNA: mechanism and correlation diagrams

The basic mechanistic traits of the main photochemical reactions in DNA, the formation of the cyclobutane and oxetane thymine dimerization adducts, are established with the help of CASSCF and CASPT2 calculations for a gas-phase model of two stacked thymines. Both reactions go through conical intersections between the ground and the excited state that are connected through minimum energy paths to the corresponding products. This explains the ultrafast formation of the cyclobutane adduct detected experimentally, and it suggests that the oxetane formation also occurs on that time scale. Moreover, the states responsible for the photoproduct formation correlate with two high-lying states of the pair in its ideal B-DNA conformation. These states are different from the delocalized states resulting from coupling of the localized ones, which suggests that the origin of the reactive electronic states lies in the pi stacking. Formation of the photoproducts requires population of these states, by direct excitation of favorable conformations, or preceded by a localized excitation.