Chromophore Structure Research Articles

Impact of Fluctuations in the Peridinin-Chlorophyll a-Protein on the Energy Transfer: Insights from Classical and QM/MM Molecular Dynamics Simulations.

The peridinin-chlorophyll a-protein is a light-harvesting complex found in dinoflagellates, which has an unusually high fraction of carotenoids. The carotenoids are directly involved in the energy transfer to chlorophyll with high efficiency. The detailed mechanism of energy transfer and the roles of the protein in the process remain debated in the literature, in part because most calculations have focused on a limited number of chromophore structures. Here we investigate the magnitude of the fluctuations of the site energies of individual and coupled chromophores, as the results are essential to the understanding of experimental spectra and the energy transfer mechanism. To this end, we sampled conformations of the PCP complex by means of classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. Subsequently we performed (supermolecular) excitation energy calculations on a statistically significant number of snapshots using TD-LC-DFT/CAM-B3LYP and the semiempirical time-dependent long-range corrected density functional tight binding (TD-LC-DFTB2) as the QM method. We observed that the magnitude of the site energy fluctuations is large compared to the differences of the site energies between the chromophores, and this also holds for the coupled chromophores. We also investigated the composition of the coupled states, the effect of coupling on the absorption spectra, as well as transition dipole moment orientations and the possibility of delocalized states with Chl a. Our study thus complements previous computational studies relying on a single structure and establishes the most prominent features of the coupled chromophores that are essential to the robustness of the energy transfer process.

Assembly of Pyrenes through a Quadruple Photochemical Cascade: Blocking Groups Allow Diversion from the Double Mallory Path to Photocyclization at the Bay Region.

We present a six-step cascade that converts 1,3-distyrylbenzenes (bis-stilbenes) into nonsymmetric pyrenes in 40-60% yields. This sequence merges photochemical steps, E,Z-alkene isomerization, a 6π photochemical electrocyclization (Mallory photocyclization); the new bay region cyclization, with two radical iodine-mediated aromatization steps; and an optional aryl migration. This work illustrates how the inherent challenges of engineering excited state reactivity can be addressed by logical design. An unusual aspect of this cascade is that the same photochemical process (the Mallory reaction) is first promoted and then blocked in different stages within a photochemical cascade. The use of blocking groups is the key feature that makes simple bis-stilbenes suitable substrates for directed double cyclization. While the first stilbene subunit undergoes a classic Mallory photocyclization to form a phenanthrene intermediate, the next ring-forming step is diverted from the conventional Mallory path into a photocyclization of the remaining alkene at the phenanthrene's bay region. Although earlier literature suggested that this reaction is unfavorable, we achieved this diversion via incorporation of blocking groups to prevent the Mallory photocyclization. The two photocyclizations are assisted by the relief of the excited state antiaromaticity. Reaction selectivity is controlled by substituent effects and the interplay between photochemical and radical reactivity. Furthermore, the introduction of donor substituents at the pendant styrene group can further extend this photochemical cascade through a radical 1,2-aryl migration. Rich photophysical and supramolecular properties of the newly substituted pyrenes illustrate the role of systematic variations in the structure of this classic chromophore for excited state engineering.

The influence of the azo chromophore structure and quantum dots on the photoinduced phase transition in a nematic liquid crystal

ABSTRACT We present an analysis of the ‘order-disorder’ phase transition into the liquid crystal matrix containing photochromic molecules with a small amount of semiconductor quantum dots (QDs). The factors studied are the influence of the chemical structure of azochromophores introduced in a liquid crystal (LC) on the phase behaviour and dielectric properties of the resulting composites as well as the life-time of the isotropic phase after photoinduced phase transition. We have chosen two azochromophores with different melting points Tm and degrees of branching. The branched structure of one chromophore promotes an increase in the life-time of Z-conformation and the corresponding stabilisation of the isotropic phase. The main factor influencing the increase in the life-time is a weaker intermolecular interaction between the LC matrix and the chromophore molecules. QDs in small amounts (0.5 and 1 wt.%) have a significantly smaller impact on the phase transition.

Interrogating the photoluminescent properties of carbon dots using quantitative 13C NMR combined with systematic photobleaching

In this work, molecular-level events accompanying the photobleaching of carbon dots (CDs) synthesized from ethylenediamine and citric acid (CACDs) were identified using solution-phase NMR. By combining quantitative 13C NMR data with fluorescence measurements we show that this new approach is capable of identifying not only molecular fluorophores in CACDs, but also their contribution to the overall CACD fluorescence and their relative photostability. Specifically, imidazo[1,2-a]pyridine-7-carboxylic acid (IPCA) is found to be the dominant (84 %) species responsible for fluorescence in CACDs along with a second undetermined source, most likely associated with the aromatic core which is significantly (approximately 20 times) more photostable than IPCA. The presence of these two fluorescent species with different photostabilities rationalizes not only the photobleaching kinetics but also the evolution of the fluorescence spectrum during photobleaching Diffusion-ordered spectroscopy (DOSY) also reveals that all of the IPCA molecules are trapped within or covalently bound to the CACD, but are not present as isolated molecules freely rotating in solution. Singlet oxygen is confirmed as a key ROS responsible for photobleaching, with prototypical photoproducts identified from mass spectrometry studies of citrazinic acid. Quantitative 13C NMR of CACDs is possible because their extremely high colloidal stability enables high concentrations (667 mg/mL) to remain stable in solution. The approach described in this study could be extended to identify the structure of chromophores in other CDs and interrogate molecular level processes that accompany CD sensing.

Efficient Synthesis of the Pyoverdine Chromophore: Expanding the Toolbox for the Preparation of Pyoverdine Conjugates

AbstractThe pyoverdine chromophore is an important component of a family of siderophores which are secreted by the human pathogen Pseudomonas aeruginosa for iron absorption. In this study, an efficient and improved synthetic route to the chromophore structure is reported, beginning from readily available starting materials, D‐glutamic acid and L–DOPA. This strategy has not only delivered the first synthesis of the free pyoverdine D chromophore, but also offers potential access to a wide range of other pyoverdine chromophore species.

Study on the extraction of Phycocyanin and the impact of in vitro simulated digestion on its anti-diabetic ability

Phycocyanin (PC) has significant anti-diabetic activity. However, research on the impact of digestion on the anti-diabetic properties of PC is still rare. In this study, we successfully extracted food-grade PC with a purity of 1.64 ± 0.06 from Ge Xian Mi. The results of antioxidant and enzyme activity inhibition experiments indicate that the biological activity of PC is positively correlated with its purity. Fluorescence and UV–Vis spectroscopy revealed the degradation of apolipoprotein and chromophore structures in PC during digestion. During digestion, the characteristic peaks of chromophores gradually disappeared, accompanied by a continuous decrease in antioxidant activity. The results of secondary structure determination indicate that after 0.5 h of digestion, the α-helix content decreased by approximately 50%, while the β-sheet content decreased by 6.87%. At the end of digestion, the α-helix structure was completely lost. The inhibitory effect of PC on the two enzymes decreased by approximately 20% after digestion started, followed by a rebound at 1.0 h, and then declined again at 3.0 h. At the end of digestion, the inhibition rates against α-amylase and α-glucosidase were only 22.09% and 25.76%, respectively. Digestion significantly decreased the antidiabetic ability of PC.

Chromophore Structural Change during the Photocycle of a Light-Driven Cl- Pump from Mastigocladopsis repens: A Cryogenic Raman Study.

Microbial rhodopsins are the most widely distributed photoreceptors that bind a retinal Schiff base chromophore. Among them, a light-driven Cl- pump discovered from Mastigocladopsis repens (MrHR) is distinctive in that it has the structural features of both H+ and Cl- pumps. While the photocycle has been characterized by light-induced changes of the absorption spectrum, the structural changes of the retinal chromophore remain largely unknown. In this study, we examined the chromophore structural changes of MrHR by using cryogenic Raman spectroscopy. We observed five photointermediates─K, L, N1, N2, and MrHR'─that show distinct vibrational spectra, indicating atypical chromophore structures, e.g., small distortion in the K intermediate and Schiff base configurational change in the MrHR' intermediate. Based on the Raman spectra of two N intermediates (N1 and N2), we propose that N1 is the Cl--bound state and N2 is the Cl--unbound state, which are responsible for the Cl- release and uptake, respectively, to achieve Cl- pumping.

Prospects of phycoerythrin: Structural features, antioxidation and applications in food

Phycoerythrin (PE) is a naturally occurring plant protein of algal origin. The colour, bioactivity and stability of PE are inextricably linked to its structure. PE has powerful antioxidant properties that effectively prevent oxidative stress and cellular damage, for which the chromophore structure plays a key role. However, the relationship between the chromophore and thermal stability is unclear in PE. The environmental factors affecting the thermal stability of PE are mainly light, high temperature and extreme pH. PE stability can be enhanced through various techniques, including the incorporation of additives, cross-linking processes, and the formation of complexes. Improving the stability of PE is of significant importance for its applications within the food industry. This paper outlines the structural characteristics of PE, discusses the relationship between its structure and antioxidant activity, and focuses on the application of PE in the food industry, as well as the factors affecting its stability and strategies for its improvement.

Novel Functional Organic Chromophores

Porphyrins and other tetrapyrroles are highly suitable for sensing operations based on their synthetic flexibility and chromophore structures where an analyte might interact to stimulate some variation in directly observable optical colour or fluorescence emission modulation. Their chromophore structures also allow access to electronic triplet states, which can be harnessed for the generation of singlet oxygen – a highly reactive species useful for photodynamic action against tumours or microorganisms. Here we discuss the sensing activity of several β-substituted porphyrins1 including not only by the introduction of suitable interacting units but also by the adaptation of non-planar porphyrins for the synthesis of porous structures. The latter are applied for film formation and sensing involving nanomechanical sensors. Selectivity and mechanisms of sensing activity are discussed. We will also introduce new efficient singlet oxygen generating materials based on agglomeration of an oxidized porphyrin chromophore as metal-organic frameworks,2 electron deficient porous polymers, or using resorcinarenes.3 The use of these materials for selective oxidation of organic substrates is demonstrated. Overall, the results demonstrate the efficacy of the chromophore approach to functional materials. The self-assembly properties of porphyrins and nitrogen rich acene compounds, the pyrazinacenes, will also be considered based on contrasting cases of on-surface mobility and immobility, and the introduction of particular functionality influencing the resulting supramolecular structures.

FTIR study of light-induced proton transfer and Ca2+ binding in T82D mutant of TAT rhodopsin

Proton transfer reactions play important functional roles in many proteins, such as enzymes and transporters, which is also the case in rhodopsins. In fact, functional expression of rhodopsins accompanies intramolecular proton transfer reactions in many cases. One of the exceptional cases can be seen in the protonated form of marine bacterial TAT rhodopsin, which isomerizes the retinal by light but returns to the original state within 10−5 s. Thus, light energy is converted into heat without any function. In contrast, the T82D mutant of TAT rhodopsin conducts the light-induced deprotonation of the Schiff base at high pH. In this article, we report the structural analysis of T82D by means of difference Fourier transform infrared (FTIR) spectroscopy. In the light-induced difference FTIR spectra at 77 K, we observed little hydrogen out-of-plane vibrations for T82D as well as the wild-type (WT), suggesting that the planar chromophore structure itself is not the origin of the reversion from the K intermediate in WT TAT rhodopsin. Upon relaxation of the K intermediate, T82D forms the following intermediate, such as M, whereas K of WT returns to the original state. Present FTIR analysis revealed the proton transfer from the Schiff base to D82 in T82D upon formation of the M intermediate. It is accompanied by the second proton transfer from E54 to the Schiff base, forming the N intermediate, particularly in membranes. The equilibrium between the M and N intermediates corresponds to the protonation equilibrium between E54 and the Schiff base. We also found that Ca2+ binding takes place in T82D as well as WT but with 6 times lower affinity. An altered hydrogen-bonding network would be the origin of low affinity in T82D, where deprotonation of E54 is involved in the Ca2+ binding.

Bioinspired Three-Component System to Prepare Full-Color Functional Biomimetic Pigments.

Nature provides a great source of inspiration for the development of sustainable materials with excellent properties, among which melanin with optical, electronic, and radiation protection properties are considered to be promising coloring materials. However, compared to chemical pigments, the single color, complex oxidation process, and poor solubility of natural melanin strongly limit their further applications. Here, we introduce a series of melanin-like polymeric pigments with amino acid-encoded physicochemical properties by a simple three-component reaction system. Our protocol enables artificial control of the chromophore structures through the rational design of the substrates and dopants, thereby combining the safety and functionality of biopigments with the color richness of chemical dyes. Similar to the photoprotective effect of natural melanin, the polymeric pigments showed excellent antioxidant activity in reducing free radicals and have the advantages of iridescent color, strong tinting strength, stability, and affordability. Furthermore, due to their ability to dye substrates, these biomimetic are expected to become new low-cost bioactive chromophores and find various biochemical applications such as in clothing and hair dyeing, food addition, and anticounterfeiting detection.

The Development of Visible-Light Organic Photocatalysts for Atom Transfer Radical Polymerization via Conjugation Extension.

This work aimed to develop organic photocatalysts (PCs) that could mediate organocatalytic atom transfer radical polymerization (O-ATRP) under visible light. Through the core-modification of known chromophoric structures and ring-locking to reach a conjugation extension, annulated N-aryl benzo[kl]acridines were identified as effective visible light-responsive photocatalysts. The corresponding selenium-doped structure showed excellent performance in the O-ATRP of methacrylates, which could afford polymer products with controlled molecular weights and low dispersities under the irradiation of visible light at a 100 ppm catalyst loading.

Substituent Effects in the Cationic Green Fluorescent Protein Chromophore: Ultrafast Excited‐State Proton Transfer or Twisting?

AbstractUnderstanding the structure‐function relationships of the green fluorescent protein (GFP) chromophore is important in rationally developing new molecular tools for biological imaging and beyond. Herein, we systematically modified the GFP chromophore structure with electron‐withdrawing and ‐donating groups (EWGs and EDGs) to investigate the substituent effects on the excited‐state proton transfer (ESPT) and twisting dynamics of the cationic chromophore in solution. With key insights gained from femtosecond transient absorption and stimulated Raman spectroscopy, we reveal that the EWG substitution by –F increases photoacidity in an additive manner and leads to an ultrafast barrierless ESPT by difluorination, while the EDG substitution by –OCH3 also results in ultrafast ESPT despite the weak photoacidity as estimated by the Förster equation. We ascribe the unusually fast kinetics in methoxylated derivatives to the occurrence of a pre‐existing chromophore‐solvent complex that sets up the acceptor site for ESPT. Furthermore, the kinetic competition between ESPT and twisting pathways is crucial for the observation of ESPT in action, particularly for molecules undergoing efficient nonradiative decay in the excited state through torsional motions. Such flexible and highly engineerable molecules can enable more versatile photoswitches and sensors.

Molecular factors determining brightness in fluorescence-encoded infrared vibrational spectroscopy.

Fluorescence-encoded infrared (FEIR) spectroscopy is a recently developed technique for solution-phase vibrational spectroscopy with detection sensitivity at the single-molecule level. While its spectroscopic information content and important criteria for its practical experimental optimization have been identified, a general understanding of the electronic and nuclear properties required for highly sensitive detection, i.e., what makes a molecule a "good FEIR chromophore," is lacking. This work explores the molecular factors that determine FEIR vibrational activity and assesses computational approaches for its prediction. We employ density functional theory (DFT) and its time-dependent version (TD-DFT) to compute vibrational and electronic transition dipole moments, their relative orientation, and the Franck-Condon factors involved in FEIR activity. We apply these methods to compute the FEIR activities of normal modes of chromophores from the coumarin family and compare these predictions with experimental FEIR cross sections. We discuss the extent to which we can use computational models to predict the FEIR activity of individual vibrations in a candidate molecule. The results discussed in this work provide the groundwork for computational strategies for choosing FEIR vibrational probes or informing the structure of designer chromophores for single-molecule spectroscopic applications.

Chromophore-Protein Interactions Affecting the Polyene Twist and π-π* Energy Gap of the Retinal Chromophore in Schizorhodopsins.

The properties of a prosthetic group are broadened by interactions with its neighboring residues in proteins. The retinal chromophore in rhodopsins absorbs light, undergoes structural changes, and drives functionally important structural changes in proteins during the photocycle. It is therefore crucial to understand how chromophore-protein interactions regulate the molecular structure and electronic state of chromophores in rhodopsins. Schizorhodopsin is a newly discovered subfamily of rhodopsins found in the genomes of Asgard archaea, which are extant prokaryotes closest to the last common ancestor of eukaryotes and of other microbial species. Here, we report the effects of a hydrogen bond between a retinal Schiff base and its counterion on the twist of the polyene chain and the color of the retinal chromophore. Correlations between spectral features revealed the unexpected fact that the twist of the polyene chain is reduced as the hydrogen bond becomes stronger, suggesting that the twist is caused by tight atomic contacts between the chromophore and nearby residues. In addition, the strength of the hydrogen bond is the primary factor affecting the color-tuning of the retinal chromophore in schizorhodopsins. The findings of this study are valuable for manipulating the molecular structure and electronic state of the chromophore by controlling chromophore-protein interactions.

Chemical Composition and Optical Properties of Secondary Organic Aerosol from Photooxidation of Volatile Organic Compound Mixtures.

The chemical and optical properties of secondary organic aerosols (SOA) have been widely studied through environmental chamber experiments, and some of the results have been parametrized in atmospheric models to help understand their radiative effects and climate influence. While most chamber studies investigate the aerosol formed from a single volatile organic compound (VOC), the potential interactions between reactive intermediates derived from VOC mixtures are not well understood. In this study, we investigated the SOA formed from pure and mixtures of anthropogenic (phenol and 1-methylnaphthalene) and/or biogenic (longifolene) VOCs using continuous-flow, high-NOx photooxidation chamber experiments to better mimic ambient conditions. SOA optical properties, including single scattering albedo (SSA), mass absorption coefficient (MAC), and refractive index (RI) at 375 nm, and chemical composition, including the formation of oxygenated organic compounds, organic-nitrogen compounds (including organonitrates and nitro-organics), and the molecular structure of the major chromophores, were explored. Additionally, the imaginary refractive index values of SOA in the multi-VOC system were predicted using a linear-combination assumption and compared with the measured values. When two VOCs were oxidized simultaneously, we found evidence for changes in SOA chemical composition compared to SOA formed from single-VOC systems, and this change led to nonlinear effects on SOA optical properties. The nonlinear effects were found to vary between different systems.

Gain of Function Recyclable Photoswitches: Reversible Simultaneous Substitution and Photochromism Generation.

The use of molecular photoswitches has spread to virtually every field of pure and applied chemistry because of the extraordinary level of control they provide over the behavior of matter at the smallest scales. Photoswitches possess at least two different states with distinct structures and/or electronics and further functionalization of their core chromophore structures is needed to tailor them for a specific application. In this work we present a different concept for the generation and use of molecular photoswitches. It allows not only simultaneous establishment of photochromism and functionalization, but also full recyclability of a non-photochromic precursor material. Using a high-yielding and reversible ammonium salt formation, a functional group is introduced into a symmetric precursor while at the same time a strong electronic push-pull character is established in the structure. The resulting desymmetrization leads to efficient photoswitching capacity and the functional group can be fully removed subsequently by a simple heating step recovering the precursor for another functionalization round. We finally demonstrate feasibility of this concept over two consecutive closed loop functionalization/photoswitching/recovery steps. This concept offers great potential in any chemical research and application driven area but especially for the creation of responsive reprogrammable materials, no-background photoswitch labeling, and sustainable chemistry.

Characterization and the Effect of Different Parameters on Photocatalytic Activity of Montmorillonite/TiO2 Nanocomposite under UVC Irradiation

This study aimed to modify montmorillonite (MMT) with titanium dioxide (TiO2) by wet stirring method combined with ultrasonic to form MMT/TiO2 nanocomposite and used as a photocatalyst in the removal of organic dye rhodamine B (RhB). The characteristics of the synthesized samples were analyzed by methods such as energy-dispersive X-ray spectroscopy (EDX), scanning electron microscope (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and UV-Vis diffuse reflectance spectra (UV-Vis DRS). The degradation of RhB was carried out for 210 min under UVC irradiation, and the decolorization efficiency of RhB was evaluated by UV-vis spectroscopy. The results show that the TiO2 anatase nanoparticles are randomly distributed on the surface or the space between the MMT sheets to form a house-of-card structure. After 210 min of exposure under a UVC light source, the decolorization efficiency reached 91.5% for the solution with pH = 6.8, photocatalyst content 0.1 g/L, initial concentration RhB 10 mg/L, and UVC power 15 W. Liquid chromatography–mass spectrometry (LCMS) identified the degradation intermediates that MMT/TiO2 successfully cleaved the chromophore structure and formed more minor broken-ring by-products. The influence of operating parameters on RhB removal efficiency, including solution pH, photocatalyst content, initial dye concentration, inorganic, and organic scavengers, was studied. In addition, the kinetic modeling study shows that the RhB photodegradation reaction is consistent with the Langmuir-Hinshelwood first-order kinetic model.

AIE‐Active Ferrocene Appended Linear (D‐π‐A) Aromatic Ester Chromophores: Structural, Theoretical and Effect on Phenyl Ring on Luminescence and Nonlinear Optical Properties

AbstractIn the present research, a new ferrocene‐appended linear donor‐π‐acceptor (D‐π‐A) ester chromophore Fc‐(C6H4)2‐COOC2H5 (2) was synthesized and characterized using various spectroscopic techniques. The molecular structure of chromophore 2 was determined using single‐crystal X‐ray diffraction analysis, revealing its crystallization in the monoclinic crystal system with the P21/n space group. The chromophore Fc‐C6H4‐COOC2H4 (1) was utilized to compare its photophysical and nonlinear optical characteristics with those of 2. Cyclic voltammetry revealed a single‐electron transfer mechanism from Fe2+↔Fe3+. The emission solvatochromism studies show a polarized excited state in response to increasing solvent polarity, indicating charge transfer processes. Interestingly, in mixed aqueous media (THF/H2O), the chromophores exhibit intensified fluorescence due to restricted intra‐molecular rotation (RIR), despite weak emission in THF solvent. Chromophore 2 demonstrated 1.5 times higher second harmonic generation (SHG) efficiency than 1, attributed to its extended π‐conjugation from an additional phenyl ring and reduced antiparallel alignments. Despite its centrosymmetric crystal packing, chromophore 2 exhibited SHG efficiency due to non‐covalent interactions (C−H⋅⋅⋅π) in the crystal lattice. Density Functional Theory (DFT) calculations, employing various functionals, provided insights into dipole moment and first hyperpolarizability, with B3LYP‐hybrid functional underestimating hyperpolarizability values owing to long‐range charge transfer interactions within the D‐π‐A systems, aligning closely with experimental findings.

Preparation and Characterisation of Nanolignin-Gelatine-Glycerol Composite (NLGGCs) Thin Film for Food Coating Application

Recognising the importance of preventing rapid food deterioration and prolonging the shelf life of fruits and vegetables from oxidation, we successfully created thin films composed of Nanolignin-Gelatine-Glycerol Composites (NLGGCs) through a traditional blending technique. Fourier Transform Infrared Spectroscopy (FTIR) confirmed the successful preparation of nanolignin structures, with characteristic peaks observed at 513 cm-1 (C-C stretching in aromatic), 1222 cm-1 (phenolic OH), and 1107 cm-1 (Ar-H and syringyl group). Ultraviolet-visible spectroscopy (UV-Vis) revealed an absorption capacity within the 280 to 300 nm range. Film opacity increased with a greater nanolignin composition in the thin film, attributed to the presence of chromophore structures. Thermogravimetric Analysis (TGA) demonstrated a thermal degradation temperature exceeding 300°C. Differential Scanning Calorimetry (DSC) analysis unveiled two distinct glass transition temperatures (Tg) at approximately 60°C and 80°C, indicating microphase separation and immiscibility between gelatine and nanolignin particles. The nanolignin content significantly influenced solubility and water uptake, with higher nanolignin content leading to reduced solubility and water absorption. The application of NLGGCs film coatings on banana surfaces extended their shelf life compared to control samples after 10 days. Furthermore, NLGGCs underscore the pivotal role in enhancing the performance as a promising bio-based food coating alternative for future applications.