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1.
Photochem Photobiol ; 97(2): 243-269, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33369749

RESUMO

This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modeling, as discussed at the CECAM workshop in Tel Aviv, Israel. The participants have identified grand challenges and discussed the development of new tools to address them. Recent progress in understanding representative proteins such as green fluorescent protein, photoactive yellow protein, phytochrome, and rhodopsin is presented, along with methodological developments.


Assuntos
Proteínas de Bactérias/química , Proteínas de Fluorescência Verde/química , Modelos Moleculares , Fotorreceptores Microbianos/química , Fitocromo/química , Rodopsina/química , Distribuição de Poisson , Teoria Quântica , Eletricidade Estática
2.
Nat Commun ; 11(1): 5682, 2020 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-33173168

RESUMO

The Rhizoclosmatium globosum genome encodes three rhodopsin-guanylyl cyclases (RGCs), which are predicted to facilitate visual orientation of the fungal zoospores. Here, we show that RGC1 and RGC2 function as light-activated cyclases only upon heterodimerization with RGC3 (NeoR). RGC1/2 utilize conventional green or blue-light-sensitive rhodopsins (λmax = 550 and 480 nm, respectively), with short-lived signaling states, responsible for light-activation of the enzyme. The bistable NeoR is photoswitchable between a near-infrared-sensitive (NIR, λmax = 690 nm) highly fluorescent state (QF = 0.2) and a UV-sensitive non-fluorescent state, thereby modulating the activity by NIR pre-illumination. No other rhodopsin has been reported so far to be functional as a heterooligomer, or as having such a long wavelength absorption or high fluorescence yield. Site-specific mutagenesis and hybrid quantum mechanics/molecular mechanics simulations support the idea that the unusual photochemical properties result from the rigidity of the retinal chromophore and a unique counterion triad composed of two glutamic and one aspartic acids. These findings substantially expand our understanding of the natural potential and limitations of spectral tuning in rhodopsin photoreceptors.


Assuntos
Quitridiomicetos/genética , Rodopsina , Biologia Computacional , Fluorescência , Corantes Fluorescentes/química , Corantes Fluorescentes/isolamento & purificação , Genes Fúngicos , Genoma Fúngico , Mutagênese Sítio-Dirigida , Processos Fotoquímicos , Células Fotorreceptoras/fisiologia , Rodopsina/biossíntese , Rodopsina/química , Rodopsina/genética
3.
J Chem Phys ; 152(21): 214117, 2020 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-32505150

RESUMO

MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

4.
Nat Chem ; 11(6): 595, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31024083

RESUMO

In the version of this Article originally published, in Fig. 5, the chemical formula Br•CC6H11 should have read Br•CH3C6H11.

5.
Photochem Photobiol ; 95(2): 662-674, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30257038

RESUMO

In this work, the electronic structure and spectroscopic properties of lumiflavin are calculated using various quantum chemical methods. The excitation energies for ten singlet and triplet states as well as the analysis of the electron density difference are assessed using various wave function-based methods and density functionals. The relative order of singlet and triplet excited states is established on the basis of the coupled cluster method CC2. We find that at least seven singlet excited states are required to assign all peaks in the UV/Vis spectrum. In addition, we have studied the solvatochromic effect on the excitation energies and found differential effects except for the first bright excited state. Vibrational frequencies as well as IR, Raman and resonance Raman intensities are simulated and compared to their experimental counterparts. We have assigned peaks, assessed the effect of anharmonicity, and confirmed the previous assignments in case of the most intense transitions. Finally, we have studied the NMR shieldings and established the effect of the solvent polarity. The present study provides data for lumiflavin in the gas phase and in implicit solvent model that can be used as a reference for the protein-embedded flavin simulations and assignment of experimental spectra.


Assuntos
Flavinas/química , Teoria Quântica , Análise Espectral/métodos
6.
Science ; 361(6398)2018 07 13.
Artigo em Inglês | MEDLINE | ID: mdl-29903883

RESUMO

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.


Assuntos
Bacteriorodopsinas/química , Bacteriorodopsinas/efeitos da radiação , Retinaldeído/química , Retinaldeído/efeitos da radiação , Ácido Aspártico/química , Transporte de Íons , Isomerismo , Conformação Proteica , Bases de Schiff/química , Fatores de Tempo , Água/química , Raios X
7.
Faraday Discuss ; 207(0): 137-152, 2018 04 17.
Artigo em Inglês | MEDLINE | ID: mdl-29393940

RESUMO

The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13[double bond, length as m-dash]C14 and C15[double bond, length as m-dash]N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13[double bond, length as m-dash]C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.


Assuntos
Simulação de Dinâmica Molecular , Teoria Quântica , Rodopsinas Microbianas/química
8.
Photochem Photobiol ; 93(3): 888-902, 2017 05.
Artigo em Inglês | MEDLINE | ID: mdl-28500703

RESUMO

In this computational work, we assessed the performance of ab initio multireference (MR) methods for the calculation of vertical excitation energies of five nucleobases: adenine, guanine, cytosine, thymine and uracil. In total, we have studied 38 singlet and 30 triplet excited states. Where possible we used the multireference configuration interaction (MRCI) method as a reference for various flavors of multireference perturbation theory to second order. In particular, we have benchmarked CASPT2, NEVPT2 and XMCQDPT2. For CASPT2, we have analyzed the single-state, multistate (MS) and extended MS variants. In addition, we have assessed the effect of the ionization potential electron affinity (IPEA) shift. For NEVPT2, we have used the partially and the strongly contracted variants. Further, we have tested the commonly used RI-CC2, RI-ADC2 and EOM-CCSD methods. Generally, we observe the following trends for singlet excited states: NEVPT2 is the closest MR method to MRCISD+Q, closely followed by CASPT2 with the default IPEA shift. The same trend is observed for triplet states, although NEVPT2 and CASPT2-IPEA are getting closer. Interestingly, the n, π* singlet excited states were described more accurately than π, π* excited states, while for triplet states the trend is inverted except for NEVPT2. This work is an important benchmark for future photochemical investigations.


Assuntos
Ácidos Nucleicos/química , Modelos Químicos
9.
Phys Chem Chem Phys ; 18(41): 28883-28892, 2016 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-27722308

RESUMO

Femtosecond transient absorption measurements powered by 40 fs laser pulses reveal that ultrafast isomerization takes place upon S1 excitation of both CH2I2 and CHBr3 in the gas phase. The photochemical conversion process is direct and intramolecular, i.e., it proceeds without caging media that have long been implicated in the photo-induced isomerization of polyhalogenated alkanes in condensed phases. Using multistate complete active space second order perturbation theory (MS-CASPT2) calculations, we investigate the structure of the photochemical reaction paths connecting the photoexcited species to their corresponding isomeric forms. Unconstrained minimum energy paths computed starting from the S1 Franck-Condon points lead to S1/S0 conical intersections, which directly connect the parent CHBr3 and CH2I2 molecules to their isomeric forms. Changes in the chemical bonding picture along the S1/S0 isomerization reaction path are described using multireference average coupled pair functional (MRACPF) calculations in conjunction with natural resonance theory (NRT) analysis. These calculations reveal a complex interplay between covalent, radical, ylidic, and ion-pair dominant resonance structures throughout the nonadiabatic photochemical isomerization processes described in this work.

10.
Nat Chem ; 7(7): 562-8, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26100804

RESUMO

'Roaming' is a new and unusual class of reaction mechanism that has recently been discovered in unimolecular dissociation reactions of isolated molecules in the gas phase. It is characterized by frustrated bond cleavage, after which the two incipient fragments 'roam' on a flat region of the potential energy surface before reacting with one another. Here, we provide evidence that supports roaming in the liquid phase. We are now able to explain previous solution-phase experiments by comparing them with new ultrafast transient absorption data showing the photoisomerization of gas-phase CHBr3. We see that, upon S0-S1 excitation, gas-phase CHBr3 isomerizes within 100 fs into the BrHCBr-Br species, which is identical to what has been observed in solution. Similar sub-100 fs isomerization is now also observed for BBr3 and PBr3 in solution upon S1 excitation. Quantum chemical simulations of XBr3 (X = B, P or CH) suggest that photochemical reactivity in all three cases studied is governed by S1/S0 conical intersections and can best be described as occurring through roaming-mediated pathways.

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