The Role of the β-Ionone Ring in the Photochemical Reaction of Rhodopsin

Medium Chain Triglycerides Promote the Uptake of β-Carotene in O/W Emulsions via Intestinal Transporter SR-B1 in Caco-2 Cells

This study aimed to elucidate the impacts of carrier oil types (long chain triglycerides (LCT), medium chain triglycerides (MCT), and orange oil (indigestible oil)) on the micellization and cellular uptake of β-carotene (BC) formulated in O/W emulsions, with an emphasis on the role of intestinal transporters. The micellization and cellular uptake of BC in the gastrointestinal tract were evaluated via an in vitro digestion model and a Caco-2 cell monolayer. And the interactions between lipids and intestinal transporters were monitored by nontargeted lipidomics, RT-PCR, and Western blot. The BC micellization rates followed a decreasing trend in emulsions: corn oil (69.47 ± 4.19%) > MCT (22.22 ± 0.89%) > orange oil (11.01 ± 2.86%), whereas the cellular uptake rate of BC was significantly higher in MCT emulsion (56.30 ± 20.13%) than in corn oil emulsion (14.01 ± 1.04%, p < 0.05). The knockdown of SR-B1 led to a 31.63% loss of BC cellular uptake from MCT micelles but had no effect on corn oil micelles. Lipidomics and transporter analysis revealed that TG (10:0/10:0/12:0) and TG (10:0/12:0/12:0) might be the fingerprint lipids that promoted the cellular absorption of BC-MCT micelles via stimulating the mRNA expression of SR-B1.

Lycopene improves maternal reproductive performance by modulating milk composition and placental antioxidative and immune status

Placental health and milk quality are important for maternal reproductive performance during pregnancy and lactation. Lycopene plays an important role in antioxidation, anti-inflammation and regulating lipid metabolism. The goal of the present study was to investigate the effects of dietary lycopene supplementation in the pig model on reproductive performance, placental health and milk composition during maternal gestation and lactation. In the present study, the litter size of live piglets was increased and the litter size of dead piglets was decreased by lycopene supplementation of the diet of sows. The litter weight at birth and weaning were increased in the lycopene group. Through placental proteomics, we enriched differentially expressed proteins (DEPs), gene ontology (GO) terms, and Kyoto encyclopedia of proteins and genomes (KEGG) pathways involved in immunity, anti-inflammation, antioxidants, and lipid metabolism and transport. Furthermore, in terms of placental health, we analyzed the levels of related enzymes, metabolites and mRNA expression in the placenta. Lycopene was shown to reduce mRNA expression and the levels of placental inflammatory factors, increase the content of immunoglobulin, improve the antioxidant capacity, and improve lipid metabolism and lipid transport in the placenta. In terms of sow milk composition, lycopene increased the levels of immunoglobulins in colostrum and lactose in colostrum and milk. Overall, the results of the present study demonstrate that dietary lycopene supplementation of sows during gestation and lactation improves the reproductive performance to a certain extent; this may be due to lycopene improving the placental health and milk composition of sows.

Trajectory surface hopping molecular dynamics simulations for retinal protonated Schiff-base photoisomerization

Global switching trajectory surface hopping molecular dynamics simulations are performed using accurate on-the-fly (TD)CAM-B3LYP/6-31G potential energy surfaces to study retinal protonated Schiff-base photoisomerization up to S₁ excitation. The simulations detected two-layer conical intersection networks: one is at an energy as high as 8 eV and the other is in the energy range around 3-4 eV. Six conical intersections within the low-layer energy region that correspond to active conical intersections under experimental conditions are found via the use of pairwise isomers, within which nonadiabatic molecular dynamics simulations are performed. Eight isomer products are populated with simulated sampling trajectories from which the simulated quantum yield in the gas phase is estimated to be 0.11 (0.08) moving from the all-trans isomer to the 11-cis (11-cis to all-trans) isomer in comparison with an experimental value of 0.09 (0.2) in the solution phase. Each conical intersection is related to one specific twist angle accompanying a related CC double bond motion during photoisomerization. Nonplanar distortion of the entire dynamic process has a significant role in the formation of the relevant photoisomerization products. The present simulation indicates that all hopping points show well-behaved potential energy surface topology, as calculated via the conventional TDDFT method, at conical intersections between S₁ and S₀ states. Therefore, the present nonadiabatic dynamics simulations with the TDDFT method are very encouraging for simulating various large systems related to retinal Schiff-base photoisomerization in the real world.

Describing ground and excited state potential energy surfaces for molecular photoswitches using coupled cluster models

In this article, we use two extensively studied systems, a retinal model system and azobenzene, to explore the use of coupled cluster models for describing ground and singlet excited state potential energy surfaces of photoswitchable systems. While not being suitable for describing nuclear dynamics of photoisomerization, coupled cluster models have useful attributes, such as the inclusion of dynamical correlation, their black box nature, and the systematic improvement offered by truncation level. Results for the studied systems show that when triple excitations (here through the CC3 model) are included, ground and excited state potential energy surfaces for isomerization paths may reliably be generated, also for states of doubly excited character. For ground state equilibrium cis- and trans-azobenzene, the molecular geometry and basis set is seen to significantly impact the vertical excitation energies for the two lowest excited states. Efficient implementations of coupled cluster models can therefore constitute valuable tools for investigating photoswitchable systems and can be used for preliminary black box studies to gather information before more complicated excited state dynamics approaches are pursued.

Health benefits of carotenoids and potential application in poultry industry: A review

Carotenoids are one of the widespread and ubiquitous lipid-soluble pigments that produce a wide range of colours which are universally found in various plants, microalgae, bacteria and fungi. Recently, interest in using carotenoids as feed ingredients has increased markedly owing to their bioactive and health-promoting properties. In terms of applications, carotenoid-rich products are widely available in the form of food and feed additive, supplements and natural colourants. Carotenoids play a versatile biological role that contributes to therapeutic effects, including anticancer, immunomodulators, anti-inflammatory, antibacterial, antidiabetic and neuroprotective. Dietary supplementation of carotenoids not only improves the production performance and health of poultry birds, but also enhances the quality of egg and meat. Several studies have suggested that the supplementation of plant derived carotenoids revealed numerous health-promoting activities in poultry birds. Carotenoids reduce the oxidative stress in pre-hatched and post-hatched birds through different mechanisms, including quench free radicals, activating antioxidant enzymes and inhibiting the signalling pathways. Use of carotenoids in poultry feed as a part of nutrient that confers bird health and improve product quality. Carotenoids play a critical role for the pigmentation of egg yolk, skin, legs, beak, comb, feather and fat. Birds consumed carotenoid deficient diet resulting hues of their egg yolk or pale coloured skin. Therefore, uniform pigmentation generally indicates the health status and quality of the poultry products. This review aims to gather recent information regarding bioactive properties of carotenoids and highlight pharmaceutical and health beneficial effects of carotenoids for the poultry industry. Additionally, it explores the importance of carotenoids as alternative feed ingredients for poultry to boost the production performance and replace synthetic medicine and nutrients.

Benchmark and performance of long-range corrected time-dependent density functional tight binding (LC-TD-DFTB) on rhodopsins and light-harvesting complexes

The chromophores of rhodopsins (Rh) and light-harvesting (LH) complexes still represent a major challenge for a quantum chemical description due to their size and complex electronic structure. Since gradient corrected and hybrid density functional approaches have been shown to fail for these systems, only range-separated functionals seem to be a promising alternative to the more time consuming post-Hartree-Fock approaches. For extended sampling of optical properties, however, even more approximate approaches are required. Recently, a long-range corrected (LC) functional has been implemented into the efficient density functional tight binding (DFTB) method, allowing to sample the excited states properties of chromophores embedded into proteins using quantum mechanical/molecular mechanical (QM/MM) with the time-dependent (TD) DFTB approach. In the present study, we assess the accuracy of LC-TD-DFT and LC-TD-DFTB for rhodopsins (bacteriorhodopsin (bR) and pharaonis phoborhodopsin (ppR)) and LH complexes (light-harvesting complex II (LH2) and Fenna-Matthews-Olson (FMO) complex). This benchmark study shows the improved description of the color tuning parameters compared to standard DFT functionals. In general, LC-TD-DFTB can exhibit a similar performance as the corresponding LC functionals, allowing a reliable description of excited states properties at significantly reduced cost. The two chromophores investigated here pose complementary challenges: while huge sensitivity to external field perturbation (color tuning) and charge transfer excitations are characteristic for the retinal chromophore, the multi-chromophoric character of the LH complexes emphasizes a correct description of inter-chromophore couplings, giving less importance to color tuning. None of the investigated functionals masters both systems simultaneously with satisfactory accuracy. LC-TD-DFTB, at the current stage, although showing a systematic improvement compared to TD-DFTB cannot be recommended for studying color tuning in retinal proteins, similar to some of the LC-DFT functionals, because the response to external fields is still too weak. For sampling of LH-spectra, however, LC-TD-DFTB is a viable tool, allowing to efficiently sample absorption energies, as shown for three different LH complexes. As the calculations indicate, geometry optimization may overestimate the importance of local minima, which may be averaged over when using trajectories. Fast quantum chemical approaches therefore may allow for a direct sampling of spectra in the near future.

From in planta Function to Vitamin-Rich Food Crops: The ACE of Biofortification

Humans are highly dependent on plants to reach their dietary requirements, as plant products contribute both to energy and essential nutrients. For many decades, plant breeders have been able to gradually increase yields of several staple crops, thereby alleviating nutritional needs with varying degrees of success. However, many staple crops such as rice, wheat and corn, although delivering sufficient calories, fail to satisfy micronutrient demands, causing the so called 'hidden hunger.' Biofortification, the process of augmenting nutritional quality of food through the use of agricultural methodologies, is a pivotal asset in the fight against micronutrient malnutrition, mainly due to vitamin and mineral deficiencies. Several technical advances have led to recent breakthroughs. Nutritional genomics has come to fruition based on marker-assisted breeding enabling rapid identification of micronutrient related quantitative trait loci (QTL) in the germplasm of interest. As a complement to these breeding techniques, metabolic engineering approaches, relying on a continuously growing fundamental knowledge of plant metabolism, are able to overcome some of the inevitable pitfalls of breeding. Alteration of micronutrient levels does also require fundamental knowledge about their role and influence on plant growth and development. This review focuses on our knowledge about provitamin A (beta-carotene), vitamin C (ascorbate) and the vitamin E group (tocochromanols). We begin by providing an overview of the functions of these vitamins in planta, followed by highlighting some of the achievements in the nutritional enhancement of food crops via conventional breeding and genetic modification, concluding with an evaluation of the need for such biofortification interventions. The review further elaborates on the vast potential of creating nutritionally enhanced crops through multi-pathway engineering and the synergistic potential of conventional breeding in combination with genetic engineering, including the impact of novel genome editing technologies.

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

The initial S₁ 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 S₁ 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.

Is the choice of a standard zeroth-order hamiltonian in CASPT2 ansatz optimal in calculations of excitation energies in protonated and unprotonated schiff bases of retinal?

To account for systematic error of CASPT2 method empirical modification of the zeroth-order Hamiltonian with Ionization Potential-Electron Affinity (IPEA) shift was introduced. The optimized IPEA value (0.25 a.u.), called standard IPEA (S-IPEA), was recommended but due to its unsatisfactory performance in multiple metallic and organic compounds it has been questioned lately as a general parameter working properly for all molecules under CASPT2 study. As we are interested in Schiff bases of retinal, an important question emerging from this conflict of choice, to use or not to use S-IPEA, is whether the introduction of the modified zeroth-order Hamiltonian into CASPT2 ansatz does really improve their energetics. To achieve this goal, we assessed an impact of the IPEA shift value, in a range of 0-0.35 a.u., on vertical excitation energies to low-lying singlet states of two protonated (RPSBs) and two unprotonated (RSBs) Schiff bases of retinal for which experimental data in gas phase are available. In addition, an effect of geometry, basis set, and active space on computed VEEs is also reported. We find, that for these systems, the choice of S-IPEA significantly overestimates both S₀ →S₁ and S₀ →S₂ energies and the best theoretical estimate, in reference to the experimental data, is provided with either unmodified zeroth-order Hamiltonian or small value of the IPEA shift in a range of 0.05-0.15 a.u., depending on active space and basis set size, equilibrium geometry, and character of the excited state. © 2018 Wiley Periodicals, Inc.

Computational study on donor–acceptor optical markers for Alzheimer's disease: a game of charge transfer and electron delocalization

The length of the conjugated double bond chain in DANIR dyes modulates the charge transfer character, non-radiative deactivation pathways and affinity for amyloid-β fibril.

Assessment of Density Functional Theory for Describing the Correlation Effects on the Ground and Excited State Potential Energy Surfaces of a Retinal Chromophore Model

In the quest for a cost-effective level of theory able to describe a large portion of the ground and excited potential energy surfaces of large chromophores, promising approaches are rooted in various approximations to the exact density functional theory (DFT). In the present work, we investigate how generalized Kohn-Sham DFT (GKS-DFT), time-dependent DFT (TDDFT), and spin-restricted ensemble-DFT (REKS) methods perform along three important paths characterizing a model retinal chromophore (the penta-2,4-dieniminium cation) in a region of near-degeneracy (close to a conical intersection) with respect to reference high-level multiconfigurational wave function methods. If GKS-DFT correctly describes the closed-shell charge transfer state, only TDDFT and REKS approaches give access to the open-shell diradical, one which sometimes corresponds to the electronic ground state. It is demonstrated that the main drawback of the usual DFT-based methods lies in the absence of interactions between the charge transfer and the diradicaloid configurations. Hence, we test a new computational scheme based on the State-averaged REKS (SA-REKS) approach, which explicitly includes these interactions into account. The State-Interaction SA-REKS (SI-SA-REKS) method significantly improves on the REKS and the SA-REKS results for the target system. The similarities and differences between DFT and wave function-based approaches are analyzed according to (1) the active space dimensions of the wave function-based methods and (2) the relative electronegativities of the allyl and protonated Schiff base moieties.

Influence of cage confinement on the photochemistry of matrix-isolated E-β-ionone: FT-IR and DFT study

β-ionone, a model compound of carotenoids ring structure, was investigated by FT-IR spectroscopy in a low-temperature argon matrix as well as using B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) quantum-chemical calculations. The spectrum of matrix-isolated E-β-ionone was analyzed and attributed to six conformers of the compound. Then, matrix-isolated E-β-ionone was submitted to UV irradiation using either a broadband source (with different cutoff filters) or a narrowband laser/MOPO system (at various wavelengths). Upon 240 nm narrowband irradiation, the formation of both Z-retro-γ-ionone and Z-β-ionone was observed, the reactant and the photoproducts being in a photostationary equilibrium. Under these conditions, the matrix environment was found to hamper subsequent reactions of Z-retro-γ-ionone and Z-β-ionone, so that this last species could be observed directly for the first time. Furthermore, the formation of Z-retro-γ-ionone was shown to occur directly via an intramolecular [1,5] H-atom shift and thereby, under the constraints imposed by the matrix confinement, the conformations assumed by this photoproduct were found to be strictly determined by those initially assumed by the reactant molecules. Broadband irradiation resulted in the completion of the reaction (disappearance of the reactant) and the sole observation of Z-retro-γ-ionone. These results imply that under these conditions the Z-β-ionone is unstable, very likely decaying to additional conformers of Z-retro-γ-ionone, as reflected in the broader bands due to this photoproduct observed in the infrared spectra of the broadband irradiated matrix.

The effect of protein environment on photoexcitation properties of retinal

Retinal is the photon absorbing chromophore of rhodopsin and other visual pigments, enabling the vertebrate vision process. The effects of the protein environment on the primary photoexcitation process of retinal were studied by time-dependent density functional theory (TDDFT) and the algebraic diagrammatic construction through second order (ADC(2)) combined with our recently introduced reduction of virtual space (RVS) approximation method. The calculations were performed on large full quantum chemical cluster models of the bluecone (BC) and rhodopsin (Rh) pigments with 165-171 atoms. Absorption wavelengths of 441 and 491 nm were obtained at the B3LYP level of theory for the respective models, which agree well with the experimental values of 414 and 498 nm. Electrostatic rather than structural strain effects were shown to dominate the spectral tuning properties of the surrounding protein. The Schiff base retinal and a neighboring Glu-113 residue were found to have comparable proton affinities in the ground state of the BC model, whereas in the excited state, the proton affinity of the Schiff base is 5.9 kcal/mol (0.26 eV) higher. For the ground and excited states of the Rh model, the proton affinity of the Schiff base is 3.2 kcal/mol (0.14 eV) and 7.9 kcal/mol (0.34 eV) higher than for Glu-113, respectively. The protein environment was found to enhance the bond length alternation (BLA) of the retinyl chain and blueshift the first absorption maxima of the protonated Schiff base in the BC and Rh models relative to the chromophore in the gas phase. The protein environment was also found to decrease the intensity of the second excited state, thus improving the quantum yield of the photoexcitation process. Relaxation of the BC model on the excited state potential energy surface led to a vanishing BLA around the isomerization center of the conjugated retinyl chain, rendering the retinal accessible for cis-trans isomerization. The energy of the relaxed excited state was found to be 30 kcal/mol (1.3 eV) above the minimum ground state energy, and might be related to the transition state of the thermal activation process.

Studies of the ground and excited-state surfaces of the retinal chromophore using CAM-B3LYP

The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.

On the primary event of phytochrome: quantum chemical comparison of photoreactions at C4, C10 and C15

Phytochromes are widespread photoreceptors responsive to red and far-red light that exist in two photochromic forms Pr (inactive) and Pfr (active). The Pr --> Pfr conversion proceeds through a series of events initiated by Z-->E photoisomerization of the tetrapyrrole chromophore, believed to occur at C15 of the methine bridge between rings C and D. Recent crystal structures show that ring D in Pr is less tightly packed by the protein than rings A, B and C, which should favor the C15 reaction over reactions at C4 (AB methine bridge) and C10 (BC). In the present work, quantum chemical methods are used to establish the intrinsic reactivity of the chromophore towards all three possible Z-->E isomerization events in the absence of steric effects and specific interactions with the protein. Using a level of theory that reproduces spectroscopic data with an accuracy of approximately 0.2 eV, it is demonstrated that isolated conditions allow the C10 photoreaction to substantially dominate. This finding suggests that the different degrees of ring-packing observed in the protein are crucial not only to facilitate a reaction at C15, but also to prevent an intrinsically more favorable reaction at C10 from taking place.

Coupled-cluster studies of the lowest excited states of the 11-cis-retinal chromophore

The first few excited states of the 11-cis-retinal (PSB11) chromophore have been studied at the coupled-cluster approximative singles and doubles (CC2) level using triple-zeta quality basis sets augmented with double sets of polarisation functions. The two lowest vertical excitation energies of 2.14 and 3.21 eV are in good agreement with recently reported experimental values of 2.03 and 3.18 eV obtained in molecular beam measurements. Calculations at the time-dependent density functional theory (TDDFT) level using the B3LYP hybrid functional yield vertical excitation energies of 2.34 and 3.10 eV for the two lowest states. Zero-point vibrational energy (ZPVE) corrections of -0.09 and -0.17 eV were deduced from the harmonic vibrational frequencies for the ground and excited states calculated at the density functional theory (DFT) and TDDFT level, respectively, using the B3LYP hybrid functional.