The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter.

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

Insight on Chirality Encoding from Small Thiolated Molecule to Plasmonic Au@Ag and Au@Au Nanoparticles.

Chiral plasmonic nanomaterials exhibiting intense optical activity are promising for numerous applications. In order to prepare those nanostructures, one strategy is to grow metallic nanoparticles in the presence of chiral molecules. However, in such approach the origin of the observed chirality remains uncertain. In this work, we expand the range of available chiral plasmonic nanostructures and we propose another vision of the origin of chirality in such colloidal systems. For that purpose, we investigated the synthesis of two core-shell Au@Ag and Au@Au systems built from gold nanobipyramid cores, in the presence of cysteine. The obtained nanoparticles possess uniform shape and size and show plasmonic circular dichroism in the visible range, and were characterized by electron microscopy, circular dichroism, and UV-vis-NIR spectroscopy. Opto-chiral responses were found to be highly dependent on the morphology and the plasmon resonance. It revealed (i) the importance of the anisotropy for Au@Au nanoparticles and (ii) the role of the multipolar modes for Au@Ag nanoparticles on the way to achieve intense plasmonic circular dichroism. The role of cysteine as shaping agent and as chiral encoder was particularly evaluated. Our experimental results, supported by theoretical simulations, contrast the hypothesis that chiral molecules entrapped in the nanoparticles determine the chiral properties, highlighting the key role of the outmost part of the nanoparticles shell on the plasmonic circular dichroism. Along with these results, the impact of enantiomeric ratio of cysteine on the final shape suggested that the presence of a chiral shape or chiral patterns should be considered.

Excited-State Absorption of Uracil in the Gas Phase: Mapping the Main Decay Paths by Different Electronic Structure Methods.

We present a computational study of the one-photon and excited-state absorption (ESA) from the two lowest energy excited states of uracil in the gas phase: an nπ* dark state (1n) and the lowest energy bright ππ* state (1π). The predictions of six different linear response electronic structure methods, namely, TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, ADC(2), ADC(2)-x, and ADC(3) are critically compared. In general, the spectral shapes predicted by TD-CAM-B3LYP, EOM-CCSD, EOM-CC3, and ADC(3) are fairly similar, though the quality of TD-CAM-B3LYP slightly deteriorates in the high-energy region. By computing the spectra at some key structures on different potential energy surfaces (PES), that is, the Franck-Condon point, the 1n minimum, and structures representative of different regions of the 1π PES, we obtain important insights into the shift of the ESA spectra, following the motion of the wavepacket on the excited-state PES. Though 1π has larger ESA than 1n, some spectral regions are dominated by these latter signals. Aside from its methodological interest, we thus obtain interesting indications to interpret transient absorption spectra to disentangle the photoactivated dynamics of nucleobases.

Near-Ultraviolet Circular Dichroism and Two-Dimensional Spectroscopy of Polypeptides.

A fully quantitative theory of the relationship between protein conformation and optical spectroscopy would facilitate deeper insights into biophysical and simulation studies of protein dynamics and folding. In contrast to intense bands in the far-ultraviolet, near-UV bands are much weaker and have been challenging to compute theoretically. We report some advances in the accuracy of calculations in the near-UV, which were realised through the consideration of the vibrational structure of the electronic transitions of aromatic side chains.

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate.

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.

Two-Dimensional Electronic Spectroscopy of Benzene, Phenol, and Their Dimer: An Efficient First-Principles Simulation Protocol.

First-principles simulations of two-dimensional electronic spectroscopy in the ultraviolet region (2DUV) require computationally demanding multiconfigurational approaches that can resolve doubly excited and charge transfer states, the spectroscopic fingerprints of coupled UV-active chromophores. Here, we propose an efficient approach to reduce the computational cost of accurate simulations of 2DUV spectra of benzene, phenol, and their dimer (i.e., the minimal models for studying electronic coupling of UV-chromophores in proteins). We first establish the multiconfigurational recipe with the highest accuracy by comparison with experimental data, providing reference gas-phase transition energies and dipole moments that can be used to construct exciton Hamiltonians involving high-lying excited states. We show that by reducing the active spaces and the number of configuration state functions within restricted active space schemes, the computational cost can be significantly decreased without loss of accuracy in predicting 2DUV spectra. The proposed recipe has been successfully tested on a realistic model proteic system in water. Accounting for line broadening due to thermal and solvent-induced fluctuations allows for direct comparison with experiments.

Tetrapeptide unfolding dynamics followed by core-level spectroscopy: a first-principles approach.

In this work we demonstrate that core level analysis is a powerful tool for disentangling the dynamics of a model polypeptide undergoing conformational changes in solution and disulphide bond formation. In particular, we present computer simulations within both initial and final state approximations of 1s sulphur core level shifts (S1s CLS) of the CYFC (cysteine-phenylalanine-tyrosine-cysteine) tetrapeptide for different folding configurations. Using increasing levels of accuracy, from Hartree-Fock and density functional theory to configuration interaction via a multiscale algorithm capable of reducing drastically the computational cost of electronic structure calculations, we find that distinct peptide arrangements present S1s CLS sizeably different (in excess of 0.5 eV) with respect to the reference disulfide bridge state. This approach, leading to experimentally detectable signals, may represent an alternative to other established spectroscopic techniques.

Tracking conformational dynamics of polypeptides by nonlinear electronic spectroscopy of aromatic residues: a first-principles simulation study.

The ability of nonlinear electronic spectroscopy to track folding/unfolding processes of proteins in solution by monitoring aromatic interactions is investigated by first-principles simulations of two-dimensional (2D) electronic spectra of a model peptide. A dominant reaction pathway approach is employed to determine the unfolding pathway of a tetrapeptide, which connects the initial folded configuration with stacked aromatic side chains and the final unfolded state with distant noninteracting aromatic residues. The π-stacking and excitonic coupling effects are included through ab initio simulations based on multiconfigurational methods within a hybrid quantum mechanics/molecular mechanics scheme. It is shown that linear absorption spectroscopy in the ultraviolet (UV) region is unable to resolve the unstacking dynamics characterized by the three-step process: T-shaped→twisted offset stacking→unstacking. Conversely, pump-probe spectroscopy can be used to resolve aromatic interactions by probing in the visible region, the excited-state absorptions (ESAs) that involve charge-transfer states. 2D UV spectroscopy offers the highest sensitivity to the unfolding process, by providing the disentanglement of ESA signals belonging to different aromatic chromophores and high correlation between the conformational dynamics and the quartic splitting.

Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car-Parrinello and TDDFT/CASPT2 Calculations.

We present Car-Parrinello and Car-Parrinello/molecular mechanics simulations of the structural, vibrational, and electronic properties of formaldehyde in water. The calculated properties of the molecule reproduce experimental values and previous calculations. The n → π* excitation energy, calculated with TDDFT and CASPT2, agrees with experimental data. In particular, it shows a blue shift on going from the gas phase to aqueous solution. Temperature and wave function polarization contributions have been disentangled.

Triplet pathways in diarylethene photochromism: photophysical and computational study of dyads containing ruthenium(II) polypyridine and 1,2-bis(2-methylbenzothiophene-3-yl)maleimide units.

A 1,2-bis(2-methylbenzothiophene-3-yl)maleimide model ( DAE) and two dyads in which this photochromic unit is coupled, via a direct nitrogen-carbon bond ( Ru-DAE) or through an intervening methylene group ( Ru-CH 2-DAE ), to a ruthenium polypyridine chromophore have been synthesized. The photochemistry and photophysics of these systems have been thoroughly characterized in acetonitrile by a combination of stationary and time-resolved (nano- and femtosecond) spectroscopic methods. The diarylethene model DAE undergoes photocyclization by excitation at 448 nm, with 35% photoconversion at stationary state. The quantum yield increases from 0.22 to 0.33 upon deaeration. Photochemical cycloreversion (quantum yield, 0.51) can be carried out to completion upon excitation at lambda > 500 nm. Photocyclization takes place both from the excited singlet state (S 1), as an ultrafast (ca. 0.5 ps) process, and from the triplet state (T 1) in the microsecond time scale. In Ru-DAE and Ru-CH 2-DAE dyads, efficient photocyclization following light absorption by the ruthenium chromophore occurs with oxygen-sensitive quantum yield (0.44 and 0.22, in deaerated and aerated solution, respectively). The photoconversion efficiency is almost unitary (90%), much higher than for the photochromic DAE alone. Efficient quenching of both Ru-based MLCT phosphorescence and DAE fluorescence is observed. A complete kinetic characterization has been obtained by ps-ns time-resolved spectroscopy. Besides prompt photocyclization (0.5 ps), fast singlet energy transfer takes place from the excited diarylethene to the Ru(II) chromophore (30 ps in Ru-DAE, 150 ps in Ru-CH 2-DAE ). In the Ru(II) chromophore, prompt intersystem crossing to the MLCT triplet state is followed by triplet energy transfer to the diarylethene (1.5 ns in Ru-DAE, 40 ns in Ru-CH 2-DAE ). The triplet state of the diarylethene moiety undergoes cyclization in a microsecond time scale. The experimental results are complemented with a combined ab initio and DFT computational study whereby the potential energy surfaces (PES) for ground state (S 0) and lowest triplet state (T 1) of the diarylethene are investigated along the reaction coordinate for photocyclization/cycloreversion. At the DFT level of theory, the transition-state structures on S 0 and T 1 are similar and lean, along the reaction coordinate, toward the closed-ring form. At the transition-state geometry, the S 0 and T 1 PES are almost degenerate. Whereas on S 0 a large barrier (ca. 45 kcal mol (-1)) separates the open- and closed-ring minima, on T 1 the barriers to isomerization are modest, cyclization barrier (ca. 8 kcal mol (-1)) being smaller than cycloreversion barrier (ca. 14 kcal mol (-1)). These features account for the efficient sensitized photocyclization and inefficient sensitized cycloreversion observed with Ru-DAE. Triplet cyclization is viewed as a nonadiabatic process originating on T 1 at open-ring geometry, proceeding via intersystem crossing at transition-state geometry, and completing on S 0 at closed-ring geometry. A computational study of the prototypical model 1,2-bis(3-thienyl)ethene is used to benchmark DFT results against ab initio CASSCF//CASPT2 results and to demonstrate the generality of the main topological features of the S 0 and T 1 PES obtained for DAE. Altogether, the results provide strong experimental evidence and theoretical rationale for the triplet pathway in the photocyclization of photochromic diarylethenes.

Computational DFT investigation of vicinal amide group anchimeric assistance in ether cleavage.

Density functional theory (DFT) computations in solvent have been used to investigate the mechanism of anchimeric assistance (by a vicinal amide group) in the acid-induced ether cleavage. The calculations were carried out at the B3LYP/6-31G* level of theory via full geometry optimizations within the IEF-PCM continuum solvent model. Two different mechanisms have been investigated here that were previously hypothesized for the rate-determining step of this process: the first (mechanism A1) involves a protonated amide and an ethereal oxygen as the nucleophile, while the second (mechanism A2) involves protonation of the ethereal oxygen followed by a nucleophilic attack of the amide. Computations clearly show that the second (involving protonation of the less basic site) is the most favorite route and leads to the formation of an oxazolidinic intermediate that triggers ether hydrolysis. Results are produced that are in excellent agreement with the experiments, and a rationale for them is provided, which represents a general interpretative basis for similar anchimerically assisted processes, such as the ones characterizing the glycosidic activity of two very important classes of enzymes: beta-hexosaminidases and O-GlcNAcases.

Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone "handle" and alkyl group effect.

The low-lying singlet states (i.e. S0, S1, and S2) of the chromophore of rhodopsin, the protonated Schiff base of 11-cis-retinal (PSB11), and of its all-trans photoproduct have been studied in isolated conditions by using ab initio multiconfigurational second-order perturbation theory. The computed spectroscopic features include the vertical excitation, the band origin, and the fluorescence maximum of both isomers. On the basis of the S0-->S1 vertical excitation, the gas-phase absorption maximum of PSB11 is predicted to be 545 nm (2.28 eV). Thus, the predicted absorption maximum appears to be closer to that of the rhodopsin pigment (2.48 eV) and considerably red-shifted with respect to that measured in solution (2.82 eV in methanol). In addition, the absorption maxima associated with the blue, green, and red cone visual pigments are tentatively rationalized in terms of the spectral changes computed for PSB11 structures featuring differently twisted beta-ionone rings. More specifically, a blue-shifted absorption maximum is explained in terms of a large twisting of the beta-ionone ring (with respect to the main conjugated chain) in the visual S-cone (blue) pigment chromophore. In contrast, the chromophore of the visual L-cone (red) pigment is expected to have a nearly coplanar beta-ionone ring yielding a six double bond fully conjugated framework. Finally, the M-cone (green) chromophore is expected to feature a twisting angle between 10 and 60 degrees. The spectroscopic effects of the alkyl substituents on the PSB11 spectroscopic properties have also been investigated. It is found that they have a not negligible stabilizing effect on the S1-S0 energy gap (and, thus, cause a red shift of the absorption maximum) only when the double bond of the beta-ionone ring conjugates significantly with the rest of the conjugated chain.

A simple approach for improving the hybrid MMVB force field: application to the photoisomerization of s-cis butadiene.

MMVB is a QM/MM hybrid method, consisting of a molecular mechanics force field coupled to a valence bond Heisenberg Hamiltonian parametrized from ab initio CASSCF calculations on several prototype molecules. The Heisenberg Hamiltonian matrix elements Q(ij) and K(ij), whose expressions are partitioned here into a primary contribution and second-order correction terms, are calculated analytically in MMVB. When the original MMVB force field fails to produce potential energy surfaces accurate enough for dynamics calculations, we show that significant improvements can be made by refitting the second-order correction terms for the particular molecule(s) being studied. This "local" reparametrization is based on values of K(ij) extracted (using effective Hamiltonian techniques) from CASSCF calculations on the same molecule(s). The method is demonstrated for the photoisomerization of s-cis butadiene, and we explain how the correction terms that enabled a successful MMVB dynamics study [Garavelli, M.; Bernardi, F.; Olivucci, M.; Bearpark, M. J.; Klein, S.; Robb, M. A. J Phys Chem A 2001, 105, 11496] were refitted.