Toward a computational photobiology

Sinicropi, Adalgisa; Andruniów, Tadeusz; Vico, Luca De; Ferré, Nicolas; Olivucci, Massimo

doi:10.1351/pac200577060977

Cited by 11 publications

(12 citation statements)

References 43 publications

(49 reference statements)

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“…Additional efforts (see, for instance, [9, 38, 39] for details) are spent on optimizing the orbitals entering the multiconfigurational wavefunctions to make these orbitals suitable "on average" for the ground and excited electronic states and for the optimal choice of the number of orbitals occupied by electrons in the ground and excited state. Thus, we arrive to the CASSCF method with state-averaging, SA-CASSCF, which seems to be the most basic one for calculating the excited state potential surfaces of organic chromophores.…”

Section: Quantum Chemistry Of Chromophores In the Gas Phase And In Somentioning

confidence: 99%

“…The first review of earlier calculations is most likely due to Helms [ 36 ]; one of the most recent discussions of the achievements of quantum chemistry for the chromophores in vacuo is presented [ 37 ]. The methodology aspects of quantum chemical approximations suitable for modeling photochemical processes with organic molecules are clearly presented in the review articles [ 9 , 38 , 39 ]. To avoid getting mired into quantum chemistry terminology and the details of different approximations used presently for computer calculations of the properties of organic chromophores in the ground and excited states, we limit ourselves to a superficial description of the most common approaches.…”

Section: Quantum Chemistry Of Chromophores In the Gas Phase And In Somentioning

confidence: 99%

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Computer Modeling of the Structure and Spectra of Fluorescent Proteins

2009

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Fluorescent proteins from the family of green fluorescent proteins are intensively used as biomarkers in living systems. The chromophore group based on the hydroxybenzylidene-imidazoline molecule, which is formed in nature from three amino-acid residues inside the protein globule and well shielded from external media, is responsible for light absorption and fluorescence. Along with the intense experimental studies of the properties of fluorescent proteins and their chromophores by biochemical, X-ray, and spectroscopic tools, in recent years, computer modeling has been used to characterize their properties and spectra. We present in this review the most interesting results of the molecular modeling of the structural parameters and optical and vibrational spectra of the chromophorecontaining domains of fluorescent proteins by methods of quantum chemistry, molecular dynamics, and combined quantum-mechanical-molecular-mechanical approaches. The main emphasis is on the correlation of theoretical and experimental data and on the predictive power of modeling, which may be useful for creating new, efficient biomarkers.

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Section: Quantum Chemistry Of Chromophores In the Gas Phase And In Somentioning

confidence: 99%

Section: Quantum Chemistry Of Chromophores In the Gas Phase And In Somentioning

confidence: 99%

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

2009

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“…In recent years, the commonly used ab initio method for excited states has been the CASSCF method, for which solvation models are available [185]. CASPT2 and MRCI can treat transition energies with quantitative accuracy, and the first can be used to locate CIs [186][187][188]. The CC method was also found to give good results on transition energies for a large set of molecules, but, statistically speaking, the best theoretical estimate and closest to the experimental values remain the CASPT2 results [189].…”

Section: Methodsmentioning

confidence: 99%

“…This can be best evidenced by calculating other critical points on the excited-state PES besides the minimum, as, for instance, TS. A somewhat exotic feature of excited states, but a feature that has gained increasing importance in elucidating their dynamics, is localization of CIs [186,210,211]. They are considered to provide an ultrafast non-radiative decay path to the ground state.…”

Section: H-bond-induced Changes In the Excited-state Propertiesmentioning

confidence: 99%

Solute–Solvent Hydrogen Bond Formation in the Excited State. Experimental and Theoretical Evidence

Matei

Ionescu

Hillebrand

2010

Hydrogen Bonding and Transfer in the Excited State

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Hydrogen bonds (H-bonds) are of great importance in biological systems, as they are responsible for the secondary structure of proteins and nucleic acids and are also involved in the mechanisms of enzyme catalysis. Supramolecular chemistry makes use of H-bonds in building up novel compounds of various architectures.The identification of these interactions and the analysis of their influence on the photophysical properties are also important in designing new fluorophores for different applications, the processes involved being rather complex in nature and often only partially understood.The main feature reflecting H-bond interaction in both the ground and excited states is the solvatochromic effect on the absorption and fluorescence spectra. This implies that changes in the solvent nature or composition produce shifts in the position, shape and intensity of the spectral bands. The source of solvatochromic shifts is the different solvation of the ground and excited states: depending on the relative stabilization of these states by solvents, bathochromic (positive)or hypsochromic (negative)shifts of the maximum of the band can be observed experimentally. Thus, such changes are indicative of the interactions occurring between the solute and the solvent in its immediate vicinity. The solute-solvent interactions are classified into:1. non-specific interactions caused by polarity/polarizability effects; 2. specific interactions, such as H-bonds.

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“…Sub‐picosecond timescale of the photoisomerization in rhodopsin's native and artificial chromophores requires the usage of computational chemistry tools to deepen understanding of its mechanism . It seems that the most extensively utilized molecular modeling methodology in RPSB studies, both in vacuo and in the protein environment, is geometry optimization at the complete active space self‐consistent field (CASSCF) level of theory, followed by CASSCF‐based second‐order perturbation theory (CASPT2) energy calculation, i.e.…”

Section: Introductionmentioning

confidence: 99%

Initial excited‐state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations

Grabarek

Andruniów

2018

J Comput Chem

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The initial S excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers. Therefore, a strong coupling between bonds length inversion and backbone out-of-plane deformation resulting in a very steep S energy profile predicted by CASSCF/CASPT2 calculations is in clear contradiction with the reference XMCQDPT2 results. Even though CC2 method predicts good quality ground-state structures, the excited-state structures display more advanced torsional deformation leading to ca. 0.2 eV exaggerated energy relaxation and significantly red shifted (0.4-0.7 eV) emission maxima. According to our findings, the initial photoisomerization process in locked-11.8, and possibly in other RPSB analogs, studied fully (both geometries and energies) by multireference perturbation theory may be somewhat slower than predicted by CASSCF/CASPT2 or CC2 methods. © 2018 Wiley Periodicals, Inc.

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Toward a computational photobiology

Abstract: In this paper, we discuss the results of our recent studies on the molecular mechanism, which stand at the basis of the photochemical processes occurring in photobiological systems. These results are obtained using modern, robust, and fairly accurate high-level quantum chemical methods.

Cited by 11 publications

References 43 publications

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

Solute–Solvent Hydrogen Bond Formation in the Excited State. Experimental and Theoretical Evidence

Initial excited‐state relaxation of locked retinal protonated schiff base chromophore. An insight from coupled cluster and multireference perturbation theory calculations

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