Photodynamics of All-trans Retinal Protonated Schiff Base in Bacteriorhodopsin and Methanol Solution

Machine Learning Enables Highly Accurate Predictions of Photophysical Properties of Organic Fluorescent Materials: Emission Wavelengths and Quantum Yields

The development of functional organic fluorescent materials calls for fast and accurate predictions of photophysical parameters for processes such as high-throughput virtual screening, while the task is challenged by the limitations of quantum mechanical calculations. We establish a database covering >4300 solvated organic fluorescent dyes with 3000 distinct compounds and develop a new machine learning approach aimed at efficient and accurate predictions of emission wavelength and photoluminescence quantum yield (PLQY). Our feature engineering has given rise to a functionalized structure descriptor (FSD) and a comprehensive general solvent descriptor (CGSD), whereby a highly black-box computational framework is realized with consistently good accuracy across different dye families, ability of describing substitution effects and solvent effects, efficiency for large-scale predictions, and workability with on-the-fly learning. Evaluations with unseen molecules suggest a remarkable mean absolute error of 0.13 for PLQY and 0.080 eV for emission energy, the latter comparable to time-dependent density functional theory (TD-DFT) calculations. An online prediction platform was constructed based on the ensemble model to make predictions in various solvents. Our statistical learning methodology will complement quantum mechanical calculations as an efficient alternative approach for the prediction of these parameters.

Unusual KIE and dynamics effects in the Fe-catalyzed hetero-Diels-Alder reaction of unactivated aldehydes and dienes

Hetero-Diels-Alder (HDA) reaction is an important synthetic method for many natural products. An iron(III) catalyst was developed to catalyze the challenging HDA reaction of unactivated aldehydes and dienes with high selectivity. Here we report extensive density-functional theory (DFT) calculations and molecular dynamics simulations that show effects of iron (including its coordinate mode and/or spin state) on the dynamics of this reaction: considerably enhancing dynamically stepwise process, broadening entrance channel and narrowing exit channel from concerted asynchronous transition states. Also, our combined computational and experimental secondary KIE studies reveal unexpectedly large KIE values for the five-coordinate pathway even with considerable C-C bond forming, due to equilibrium isotope effect from the change in the metal coordination. Moreover, steric and electronic effects are computationally shown to dictate the C=O chemoselectivity for an α,β-unsaturated aldehyde, which is verified experimentally. Our mechanistic study may help design homogeneous, heterogeneous and biological catalysts for this challenging reaction.

Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins

Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.

Theoretical description of protein field effects on electronic excitations of biological chromophores

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems.

Mechanism of ultrafast non-reactive deactivation of the retinal chromophore in non-polar solvents

Counterion sensitive photodynamics of the retinal chromophore in solution.

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 cis-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 cis-DFHBDI chromophore and nearby nucleotides facilitate its binding to Spinach and further inhibit the cis-trans photoisomerization of DFHBDI. Solvent molecules, ions, and loss of key hydrogen bonds with nearby nucleotides could induce dissociation of the anionic trans-DFHBDI chromophore from the binding site. These results provide new insights into fluorescent RNA Spinach and may help rational design of other fluorescent RNAs.

A biomimetic molecular switch at work: coupling photoisomerization dynamics to peptide structural rearrangement

A combined experimental and computational study of a peptide-linked retinal-like molecular switch shows the effects on photoreactivity and the α-helix structure.

High contrast off–on fluorescence photo-switching via copper ion recognition, trans–cis isomerization and ring closure of a thiosemicarbazide Schiff base

Two independently addressable photochromic systems based on distinct mechanisms and selective recognition for Cu²⁺were investigated in detail.

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 trans-[Ru(tpy)(pynp)(OH2)](2+) (TA) and cis-[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 (TMLCT) and the other from a triplet metal-centered d-d transition (TMC). The vertical excitation of the singlet ground state of the complexes leads to a singlet excited state, which undergoes ultrafast decay to the corresponding TMLCT. For TA, this TMLCT transforms with a low barrier to a TMC state. The dissociative nature of the TMC 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 TMLCT is very much stabilized with a very strong Ru(II)-OH bond; the high barrier from this TMLCT blocks conversion to a TMC state and thus prevents isomerization from the cis to the trans 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 (XMC-CB, XMC-CA) near the minimum of the triplet metal-centered state of the cis isomer provide nonadiabatic decay channels to the ground-state S0--CA, which completes the photoisomerization pathway from TA to CA.

ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization

Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.