Photodynamics of All-<i>trans</i> Retinal Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution

Nonadiabatic ONIOM(CASSCF:AMBER) and CASSCF simulations elucidated different photodynamics of an all-trans retinal protonated Schiff base (RPSB) in bacteriorhodopsin and methanol as well as without an environment. The bR protein matrix holds RPSB tight via specific interactions and promotes bond-specific (along the C13C14 bond), unidirectional, and ultrafast photoisomerization with a high quantum yield. In contrast, in methanol and for the twisted bare RPSB, photoisomerization is not bond-specific (mainly along the C11C12 bond), is nonunidirectional, and is ineffective. Therefore, bR efficiently “catalyzes” photoisomerization and stores enough energy to promote the subsequent proton pumping and protein conformational changes

Multiscale Simulations on Spectral Tuning and the Photoisomerization Mechanism in Fluorescent RNA Spinach

Fluorescent RNA aptamer Spinach can bind and activate a green fluorescent protein (GFP)-like chromophore (an anionic DFHBDI chromophore) displaying green fluorescence. Spectroscopic properties, spectral tuning, and the photoisomerization mechanism in the Spinach-DFHBDI complex have been investigated by high-level QM and hybrid ONIOM­(QM:AMBER) methods (QM method: (TD)­DFT, SF-BHHLYP, SAC-CI, LT-DF-LCC2, CASSCF, or MS-CASPT2), as well as classical molecular dynamics (MD) simulations. First, our benchmark calculations have shown that TD-DFT and spin-flip (SF) TD-DFT (SF-BHHLYP) failed to give a satisfactory description of absorption and emission of the anionic DFHBDI chromophore. Comparatively, SAC-CI, LT-DF-LCC2, and MS-CASPT2 can give more reliable transition energies and are mainly used to further study the spectra of the anionic DFHBDI chromophore in Spinach. The RNA environmental effects on the spectral tuning and the photoisomerization mechanism have been elucidated. Our simulations show that interactions of the anionic <i>cis</i>-DFHBDI chromophore with two G-quadruplexes as well as a UAU base triple suppress photoisomerization of DFHBDI. In addition, strong hydrogen bonds between the anionic <i>cis</i>-DFHBDI chromophore and nearby nucleotides facilitate its binding to Spinach and further inhibit the <i>cis</i>-<i>trans</i> photoisomerization of DFHBDI. Solvent molecules, ions, and loss of key hydrogen bonds with nearby nucleotides could induce dissociation of the anionic <i>trans</i>-DFHBDI chromophore from the binding site. These results provide new insights into fluorescent RNA Spinach and may help rational design of other fluorescent RNAs

Photodynamics of All-<i>trans</i> Retinal Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution

Nonadiabatic ONIOM(CASSCF:AMBER) and CASSCF simulations elucidated different photodynamics of an all-trans retinal protonated Schiff base (RPSB) in bacteriorhodopsin and methanol as well as without an environment. The bR protein matrix holds RPSB tight via specific interactions and promotes bond-specific (along the C13C14 bond), unidirectional, and ultrafast photoisomerization with a high quantum yield. In contrast, in methanol and for the twisted bare RPSB, photoisomerization is not bond-specific (mainly along the C11C12 bond), is nonunidirectional, and is ineffective. Therefore, bR efficiently “catalyzes” photoisomerization and stores enough energy to promote the subsequent proton pumping and protein conformational changes

Photodynamics of All-<i>trans</i> Retinal Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution

Nonadiabatic ONIOM(CASSCF:AMBER) and CASSCF simulations elucidated different photodynamics of an all-trans retinal protonated Schiff base (RPSB) in bacteriorhodopsin and methanol as well as without an environment. The bR protein matrix holds RPSB tight via specific interactions and promotes bond-specific (along the C13C14 bond), unidirectional, and ultrafast photoisomerization with a high quantum yield. In contrast, in methanol and for the twisted bare RPSB, photoisomerization is not bond-specific (mainly along the C11C12 bond), is nonunidirectional, and is ineffective. Therefore, bR efficiently “catalyzes” photoisomerization and stores enough energy to promote the subsequent proton pumping and protein conformational changes

Reaction Mechanism of Photoinduced Decarboxylation of the Photoactivatable Green Fluorescent Protein: An ONIOM(QM:MM) Study

Photoactivatable (PA) fluorescent proteins are a new class of fluorescent proteins in which the intensity of fluorescence is dramatically enhanced through photoinduced decarboxylation process. In the present study, the reaction mechanism of the photoinduced decarboxylation in PA-GFP was investigated by the ONIOM­(QM:MM) method. The decarboxylation process starts from the first excited state (IntraCT state) and then proceeds along an InterCT state after the first crossing (or an approximate transition state). Relative to an equilibrium structure in S₀, a barrier of ∼94 kcal/mol to reach this approximate transition state is the rate-determining step for the entire decarboxylation process. The InterCT state becomes the open-shell ground state in the product, after the subsequent crossing with a closed-shell state that holds an extra electron on the dissociated CO₂. The present study elucidated for the first time the mechanism of the photoinduced decarboxylation of PA-GFP and supports the widely accepted Kolbe pathway, which could be a common mechanism for the irreversible photoinduced decarboxylation in different fluorescent proteins

Excited-State Proton Transfer Controls Irreversibility of Photoisomerization in Mononuclear Ruthenium(II) Monoaquo Complexes: A DFT Study

The detailed DFT investigation clears the working mechanism of the irreversible photoisomerization of <i>trans</i>-[Ru­(tpy)­(pynp)­(OH₂)]²⁺ (TA) and <i>cis</i>-[Ru­(tpy)­(pynp)­(OH₂)]²⁺ (CA) complexes. Both TA and CA complexes present two types of low lying triplet states, one resulting from a triplet metal–ligand charge-transfer (T_MLCT) and the other from a triplet metal-centered d–d transition (T_MC). The vertical excitation of the singlet ground state of the complexes leads to a singlet excited state, which undergoes ultrafast decay to the corresponding T_MLCT. For TA, this T_MLCT transforms with a low barrier to a T_MC state. The dissociative nature of the T_MC state leads to easy water removal to produce a five-coordinate intermediate that can isomerize via rotation of a pynp ligand and proceed towards the CA product. For CA, however, during this excitation and intersystem crossing process, an excited-state proton transfer (ESPT) occurs and the resultant T_MLCT is very much stabilized with a very strong Ru­(II)–OH bond; the high barrier from this T_MLCT blocks conversion to a T_MC state and thus prevents isomerization from the <i>cis</i> to the <i>trans</i> isomer. This high barrier also prevents the possibility of the isomerization process from TA to CA solely on the adiabatic triplet pathway. Instead, crossing points (X_MC‑CB, X_MC‑CA) near the minimum of the triplet metal-centered state of the <i>cis</i> isomer provide nonadiabatic decay channels to the ground-state S_0‑‑CA, which completes the photoisomerization pathway from TA to CA

A Theoretical Study on the <i>trans</i>-Addition Intramolecular Hydroacylation of 4-Alkynals Catalyzed by Cationic Rhodium Complexes

The mechanism of the intramolecular hydroacylation reaction of 4-alkynals is studied for a 4-pentynal-[Rh(PH2CH2CH2PH2)]+ model system using MP2 calculations. The endo-cyclization to form a rhodacyclohexenone intermediate is kinetically less favorable than the exo-cyclization to form a rhodacyclopentanone intermediate. The kinetic preference toward the endo-cyclization is found to be enhanced by complexation of donor ligands (H2CO, NCH, and HCCH). The formation of cyclopentenone product proceeds via reductive elimination from one of the two rhodacyclohexenone intermediates, whereas the formation of cyclobutanone product from the two rhodacyclopentanone intermediates requires high activation energy. Addition of an acetylene stabilizes the highly electron-poor rhodacyclopentanone intermediate generated from exo-cyclization and leads to an insertion to give [4 + 2] annulation product, cyclohexenone. The role of a coordinating acetone solvent in the formation of cyclopentenone product is also discussed

Quantum Tunneling in Reactions Modulated by External Electric Fields: Reactivity and Selectivity

Quantum tunneling and external electric fields (EEFs) can promote some reactions. However, the synergetic effect of an EEF on a tunneling-involving reaction and its temperature-dependence is not very clear. In this study, we extensively investigated how EEFs affect three reactions that involve hydrogen- or (ground- and excited-state) carbon-tunneling using reliable DFT, DLPNO–CCSD(T1), and variational transition-state theory methods. Our study revealed that oriented EEFs can significantly reduce the barrier and corresponding barrier width (and vice versa) through more electrostatic stabilization in transition states. These EEF effects enhance the nontunneling and tunneling-involving rates. Such EEF effects also decrease the crossover temperatures and quantum tunneling contribution, albeit with lower and thinner barriers. Moreover, EEFs can modulate and switch on/off the tunneling-driven 1,2-H migration of hydroxycarbenes under cryogenic conditions. Furthermore, our study predicts for the first time that EEF/tunneling synergy can control the chemo- or site-selectivity of one molecule bearing two similar/same reactive sites

Mechanism of Ni-NHC Catalyzed Hydrogenolysis of Aryl Ethers: Roles of the Excess Base

The transformation of aromatic carbon–oxygen (C_Ar–O) bonds in lignin to useful chemical building blocks has great potential in biomass conversion. A Ni-NHC (N-heterocyclic carbene) catalyzed selective hydrogenolysis of aryl ethers has recently been developed by Hartwig and co-worker, but the reaction mechanism, including the role of different additives found to accelerate the reaction and the origin of the selectivity, remains unclear. DFT calculations of several possible pathways for this useful and important transformation suggest a new mechanistic pathway which involves coordination of the excess base (^<i>t</i>BuO^–) to facilitate the rate-determining C–O activation step, dissociation of the ArO^– ligand, H₂ activation through a Ni–O^<i>t</i>Bu bond to give HO^<i>t</i>Bu, and finally reductive elimination to afford the arene product. Another new ion-pair (S_NAr-like) pathway for the base-assisted C–O bond activation could compete with the above base-assisted oxidative addition pathway for some diaryl ethers. The regioselective cleavage of different ethers and the effects of the Lewis acid were also examined and compared. The results demonstrate that bulkiness and strong donating ability of the NHC ligand and the presence of excess base are the keys to a Ni(0)/Ni­(II) catalytic cycle

Theoretical Study of the Intrinsic Reactivities of Various Allylmetals toward Carbonyls and Water^⊥

Quantum mechanics MP2/6-31+G* calculations have been carried out for the reactions of a series of monomeric allylmetals with water and carbonyl compounds in the gas phase. Allyl complexes of groups IA and IIA and low-valent group IIIA and IVA metals are π-complexes or reactive σ-complexes. They show high reactivities toward hydrolysis. Group IIB, trivalent group IIIA, tetravalent group IVA, and both tri- and pentavalent group VA metals form σ-complexes with allyl. These allylmetals are less reactive toward hydrolysis than toward allylation. The calculated intrinsic kinetic preference of allylation over hydrolysis is found to correlate well with the reactivity of hydrolysis, the nucleophilicity of the allylmetals, and the lateness of hydrolysis transition structures. Both the nucleophilicity of the allylmetal complexes and the thermodynamic driving force are important to the reactivity of hydrolysis. Importantly, there is a large thermodynamic preference for allylation over hydrolysis for all allylmetals because the hydrolysis has to break a strong O−H bond. Thus, the kinetic preference for allylation is correlated with the degree of H−O bond breaking in the hydrolysis transition structure