Photoreactive Molecules Research Articles

Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch.

The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet-exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the Rhodobacteraceae family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta-carotene and beta-cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria-produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water.

Radiodynamic Therapy with Photosensitizers: Mini-Review of Experimental and Clinical Studies

Photodynamic Therapy (PDT) is a light-based method that uses photo-reactive molecules, such as different types of photosensitizers (PS), to destroy malignant tumors. As some authors testify, PS was shown to act as a radio-reactive molecule by enhancing generation of reactive oxygen species upon X-ray irradiation. The method of treatment, which is based on the combined use of PS and ionizing radiation, is called «Radiodynamic therapy» (RDT). The advantage of RDT over PDT is the X-ray’s penetrability through tissues, which will find many applications for treatment of deep malignant tumors. The authors of a number of research centers in Japan, Germany, Israel and Lithuania presented the experience of using RDT in experiments on tumor cell lines and animals with transplanted tumors. A clinical approbation of the method has been started in patients with unresectable forms of bladder and cervical cancer, with gliomas and other forms of malignant tumors. The data obtained in experiments on cultures of tumor cells and animals with transplanted tumors indicate a high antitumor efficacy of the RDT with various types of PS. This fact is confirmed by a statistically significant decrease in viable tumor cells with the combined use of RT and PS, as well as a pronounced inhibition of the growth of transplanted tumors compared with the control groups, including the group of radiation therapy in mono mode. The preliminary data obtained show good tolerability of the method in clinical oncology (no serious adverse reactions) and satisfactory antitumor efficacy (an increase in the frequency of objective responses and an increase in the % reduction in tumor volume, which made it possible to transfer them to a resectable state).

Bisretinoids of the Retina: Photo-Oxidation, Iron-Catalyzed Oxidation, and Disease Consequences.

The retina and, in particular, retinal pigment epithelial cells are unusual for being encumbered by exposure to visible light, while being oxygen-rich, and also amassing photoreactive molecules. These fluorophores (bisretinoids) are generated as a byproduct of the activity of vitamin A aldehyde—the chromophore necessary for vision. Bisretinoids form in photoreceptor cells due to random reactions of two molecules of vitamin A aldehyde with phosphatidylethanolamine; bisretinoids are subsequently transferred to retinal pigment epithelial (RPE) cells, where they accumulate in the lysosomal compartment with age. Bisretinoids can generate reactive oxygen species by both energy and electron transfer, and they become photo-oxidized and photolyzed in the process. While these fluorescent molecules are accrued by RPE cells of all healthy eyes, they are also implicated in retinal disease.

A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules.

Biological liquid–liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.

Signatures of an abiotic decomposition pathway in temperate forest leaf litter

Photodegradation helps explain why leaf litter mass loss rates are comparable between mesic environments and drylands, despite water availability limiting decomposer activity in drylands. With photodegradation, light energy directly mineralizes photoreactive organic molecules such as lignin, which contrasts with biotically-driven decomposition where lignin persists in decomposing leaf litter relative to other compounds. Photodegradation of leaf litter has largely been studied in dryland systems, but whether it occurs in mesic, deciduous forest systems is uncertain. As such, we examined potential photodegradation in maple and oak litter in the Southern Appalachian Mountains (USA) during the non-growing season, when newly fallen leaves are exposed to maximum solar radiation without deciduous canopies. The proportion of oxidized lignin in the leaf litter relative to other carbon compounds decreased with maximum solar radiation during the non-growing season. With a closed canopy, however, the proportion of total lignin relative to other compounds in the leaves increased. This pattern was particularly strong for the syringyl- S6 and guaiacyl-G6 lignin monomers. The relative proportion of S6 and G6 in the litters was reduced by 10–65% in the first 5 months. The largest reductions in lignin occurred on south-facing mountain slopes where solar radiation was highest (relative to north-facing slopes) in the Northern Hemisphere. Overall, however, the changes in lignin did not alter cumulative litter mass lost. Our results suggest that photodegradation promotes the transformation and relative loss of lignin in the early stages of litter decomposition in mesic deciduous forests.

Bridging photochemistry and photomechanics with NMR crystallography: the molecular basis for the macroscopic expansion of an anthracene ester nanorod.

Crystals composed of photoreactive molecules represent a new class of photomechanical materials with the potential to generate large forces on fast timescales. An example is the photodimerization of 9-tert-butyl-anthracene ester (9TBAE) in molecular crystal nanorods that leads to an average elongation of 8%. Previous work showed that this expansion results from the formation of a metastable crystalline product. In this article, it is shown how a novel combination of ensemble oriented-crystal solid-state NMR, X-ray diffraction, and first principles computational modeling can be used to establish the absolute unit cell orientations relative to the shape change, revealing the atomic-resolution mechanism for the photomechanical response and enabling the construction of a model that predicts an elongation of 7.4%, in good agreement with the experimental value. According to this model, the nanorod expansion does not result from an overall change in the volume of the unit cell, but rather from an anisotropic rearrangement of the molecular contents. The ability to understand quantitatively how molecular-level photochemistry generates mechanical displacements allows us to predict that the expansion could be tuned from +9% to −9.5% by controlling the initial orientation of the unit cell with respect to the nanorod axis. This application of NMR-assisted crystallography provides a new tool capable of tying the atomic-level structural rearrangement of the reacting molecular species to the mechanical response of a nanostructured sample.

Photomechanical materials driven by photoisomerization or photodimerization

Light is an adjustable, multiparameter stimulus that can be used for fine, noncontact manipulation or as an energy supply. Recently, deformable light-controlled macroscopic materials have gained attention both from a fundamental research perspective and for various actuator applications. The main challenge in developing these materials is converting the photoinduced effects at the molecular level to macroscopic movements in the working pieces; a variety of mechanisms have been proposed for this. Both crystals and polymers containing photoreactive compounds have been intensively studied and have exhibited different advantages. Crosslinked liquid crystalline polymers have also attracted attention because they combine the advantages of macroscopically deformable polymers and crystals. In most circumstances, photodeformable materials contain photoreactive molecules that absorb light of a specific wavelength and thus undergo structural changes. This is followed by concomitant changes in their physical and chemical properties, resulting in macroscopic mechanical movements. Therefore, various photoreactions have been studied to induce macroscopic deformations using light. The purpose of this review is to highlight key examples in the design of photodeformable materials using various photoreactions and to introduce some new and evolving trends by highlighting recent research. Macroscopic deformable materials controlled by light have been the subject of growing research interest in the last few decades due to both their fundamental properties and their wide applicability. In this review, examples of photomechanical effects in crystals, polymers, and CLCPs based on photoisomerization and photodimerization are reviewed.

Concurrent reaction and diffusion in photo-responsive hydrogels

A hydrogel is a polymer network dispersed in an aqueous solvent. A hydrogel with photo-reactive molecules bonded on the polymer network can change its volume in response to light. The light triggers a chemical reaction of the photo-reactive molecules, for example the photo-isomerization of spirobenzopyran, and alters the interaction parameter between the polymer network and the solvent molecules, which drives the diffusion of the solvent molecules, inducing a volumetric change of the hydrogel. The photo-response kinetics of the hydrogel is governed by concurrent reaction and diffusion. In this paper, we establish a theoretical framework to describe the constitutive behavior of photo-responsive hydrogels based on non-equilibrium thermodynamics. The framework, coupling deformation of hydrogels with diffusion of solvent molecules and reaction of photo-reactive molecules, allows us to predict the spatiotemporal response of photo-responsive hydrogels under light and in the dark. We show the significantly different photo-response kinetics, including reaction-limited, diffusion-limited, and reaction-diffusion coupling processes, with constrained and free swelling of a hydrogel thin film as examples. Particularly, we demonstrate how slow diffusion postpones the onset of post-illumination kinetic response of a photo-responsive hydrogel in the dark. This framework provides us understanding and design guidelines for photo-responsive hydrogels.

Coherent Light Harvesting through Strong Coupling to Confined Light.

When photoactive molecules interact strongly with confined light modes, new hybrid light–matter states may form: the polaritons. These polaritons are coherent superpositions of excitations of the molecules and of the cavity photon. Recently, polaritons were shown to mediate energy transfer between chromophores at distances beyond the Förster limit. Here we explore the potential of strong coupling for light-harvesting applications by means of atomistic molecular dynamics simulations of mixtures of photoreactive and non-photo-reactive molecules strongly coupled to a single confined light mode. These molecules are spatially separated and present at different concentrations. Our simulations suggest that while the excitation is initially fully delocalized over all molecules and the confined light mode, it very rapidly localizes onto one of the photoreactive molecules, which then undergoes the reaction.

Quercetin and cyanidin-3-glucoside protect against photooxidation and photodegradation of A2E in retinal pigment epithelial cells

A family of photoreactive retinaldehyde-derived molecules accumulate in retinal pigment epithelial cells with age; this accumulation is implicated in some retinal diseases. One of these compounds is the diretinal fluorophore A2E. Here we compared polyphenols for their ability to suppress the photooxidation and photodegradation of A2E. In cells that had accumulated A2E and were irradiated with short-wavelength light, quercetin, cyanidin-3-glucoside, ferulic acid and chlorogenic acid diminished cellular levels of reactive oxygen species, but only quercetin and cyanidin-3-glucoside promoted cell viability. By chromatographic quantitation, quercetin and cyanidin-3-glucoside reduced the consumption of A2E by photooxidation in both cell- and cell-free assays. With ultra-high performance liquid chromatography-mass spectrometry, quercetin and cyanidin-3-glucoside also inhibited the formation of photooxidized-A2E species. While photodegradation of A2E is known to result in the release of reactive carbonyls, we demonstrated that quercetin and cyanidin-3-glucoside decreased the formation of methylglyoxal adducts in the cells, and reduced the expression of mRNA encoding receptor for advanced glycation end products. These polyphenols also protected glutathione from reaction with photooxidized A2E. In rod outer segments incubated with all-trans-retinal to generate bisretinoid, followed by irradiation, quercetin and cyanidin-3-glucoside reduced release of the lipid peroxidation product 4-hydroxynonenal. In conclusion, quercetin and cyanidin-3-glucoside can guard against photooxidative processes in retina.

Periodic potentials in hybrid van der Waals heterostructures formed by supramolecular lattices on graphene

The rise of 2D materials made it possible to form heterostructures held together by weak interplanar van der Waals interactions. Within such van der Waals heterostructures, the occurrence of 2D periodic potentials significantly modifies the electronic structure of single sheets within the stack, therefore modulating the material properties. However, these periodic potentials are determined by the mechanical alignment of adjacent 2D materials, which is cumbersome and time-consuming. Here we show that programmable 1D periodic potentials extending over areas exceeding 104 nm2 and stable at ambient conditions arise when graphene is covered by a self-assembled supramolecular lattice. The amplitude and sign of the potential can be modified without altering its periodicity by employing photoreactive molecules or their reaction products. In this regard, the supramolecular lattice/graphene bilayer represents the hybrid analogue of fully inorganic van der Waals heterostructures, highlighting the rich prospects that molecular design offers to create ad hoc materials.

A photoresponsive soft interface reversibly controls wettability and cell adhesion by conformational changes in a spiropyran-conjugated amphiphilic block copolymer.

We developed a photoresponsive polymer soft interface, which was able to spatiotemporally control wettability and cell adhesion/detachment in a reversible manner, by introducing spiropyran into the hydrophobic block of an amphiphilic diblock copolymer. With alternating irradiation using UV and visible light, the surface exhibited unique reversible wettability changes; the direction of hydrophobicity and hydrophilicity change was opposite to the polarity change in spiropyran photo-isomerization. Light-dependent reversible control of spatiotemporal cell adhesion and detachment was also achieved with sequential UV (adhesion) and visible light irradiation (detachment). Cell detachment using noncytotoxic visible light was realized for the first time. Cell-patterning capability stably lasted for 25days. This photoresponsive surface could be applied to fabrication of engineered tissues comprised of several cellular species.

Preparation of Phosphorescent Polymer Patterns by Spin‐Coating Photoreactive Small Molecules

SUMMARYPatterned polymer thin films were prepared by spin‐coating a solution consisting of an acryl monomer of 2‐(9H‐carbazol‐9‐yl)ethylmethacrylate, a photoinitiator of 4‐(dimethylamino)benzophenone, and a phosphorescent dopant of iridium(III) bis(2‐phenylpyridinate(4‐vinylphenylpyridine)). The film was exposed to ultraviolet (UV) light through a photomask and rinsed with an organic solvent to develop a patterned polymer thin film. A mixture of tetrahydrofuran and 1,4‐dioxane was used as the spin‐coating solvent, and ethanol was used as the developing solution. The effects of solvent, exposure time, UV intensity, and the phosphorescent dopant were examined to optimize the patterning condition. The patterned film was utilized as an emissive layer to construct an organic light‐emitting diode.

Near-infrared (NIR) up-conversion optogenetics.

Non-invasive remote control technologies designed to manipulate neural functions have been long-awaited for the comprehensive and quantitative understanding of neuronal network in the brain as well as for the therapy of neurological disorders. Recently, it has become possible for the neuronal activity to be optically manipulated using biological photo-reactive molecules such as channelrhodopsin (ChR)-2. However, ChR2 and its relatives are mostly reactive to visible light, which does not effectively penetrate through biological tissues. In contrast, near-infrared (NIR) light (650–1450 nm) penetrates deep into the tissues because biological systems are almost transparent to light within this so-called ‘imaging window’. Here we used lanthanide nanoparticles (LNPs), composed of rare-earth elements, as luminous bodies to activate ChRs since they absorb low-energy NIR light to emit high-energy visible light (up-conversion). Here, we created a new type of optogenetic system which consists of the donor LNPs and the acceptor ChRs. The NIR laser irradiation emitted visible light from LNPs, then induced the photo-reactive responses in the near-by cells that expressed ChRs. However, there remains room for large improvements in the energy efficiency of the LNP-ChR system.

온도에 따른 반응성 액정의 분자 배열 및 경화 반응 연구

LC242와 같이 분자량이 큰 광반응성 액정 물질은 온도를 낮출 때 액정상에서 결정으로의 변화가 빠르지 못하여 액정분자를 재결정을 할 때는 충분한 시간이 필요하다. 액정 상태에서 분자의 배열 정도가 온도에 따라 영향받는 것을 알 수 있는데, 액정상의 LC242는 온도가 높아짐에 따라 액정 배열을 한 방향으로 계속 유지하고 있어도 온도에 따른 LC242 분자들의 움직임에 의하여 조금씩 배열이 달라져 복굴절의 변화를 가져오는 것을 알 수 있다. 광반응성 액정을 경화할 때 액정 상의 온도에서 광조사를 하면 고체상의 경우보다 반응 속도가 빠르고 경화도가 훨씬 많이 진행되는 것을 Photo-DSC 실험과 FTIR을 이용하여 정량적으로 분석하였다. Since a transition from liquid crystal to crystal state is slow for the large photo-reactive liquid crystal molecules, it needs a long time for recrystallization of LC242 molecules when lowering the temperature of the liquid crystal. Although liquid crystals usually align along one direction, the directions of individual liquid crystal molecules are little different from one another with increasing temperature, resulting in changes of birefringence of the liquid crystal films. When the photo-reactive liquid crystals are photo-cured, faster curing kinetics and much larger curing degrees are observed for the films cured at the liquid crystal phase.

Ex situ and in situ characterization of patterned photoreactive thin organic surface layers using friction force microscopy.

Photolithographic methods allow an easy lateral top-down patterning and tuning of surface properties with photoreactive molecules and polymers. Employing friction force microscopy (FFM), we present here different FFM-based methods that enable the characterization of several photoreactive thin organic surface layers. First, three ex situ methods have been evaluated for the identification of irradiated and non-irradiated zones on the same organosilane sample by irradiation through different types of masks. These approaches are further extended to a time dependent ex situ FFM measurement, which allows to study the irradiation time dependent evolution of the resulting friction forces by sequential irradiation through differently sized masks in crossed geometry. Finally, a newly designed in situ FFM measurement, which uses a commercial bar-shaped cantilever itself as a noncontact shadow mask, enables the determination of time dependent effects on the surface modification during the photoreaction. SCANNING 36:590–598, 2014.

Organic Photomechanical Materials

Organic molecules can transform photons into Angstrom-scale motions by undergoing photochemical reactions. Ordered media, for example, liquid crystals or molecular crystals, can align these molecular-scale motions to produce motion on much larger (micron to millimeter) length scales. In this Review, we describe the basic principles that underlie organic photomechanical materials, starting with a brief survey of molecular photochromic systems that have been used as elements of photomechanical materials. We then describe various options for incorporating these active elements into a solid-state material, including dispersal in a polymer matrix, covalent attachment to a polymer chain, or self-assembly into molecular crystals. Particular emphasis is placed on ordered media, such as liquid-crystal elastomers and molecular crystals, that have been shown to produce motion on large (micron to millimeter) length scales. We also discuss other mechanisms for generating photomechanical motion that do not involve photochemical reactions, such as photothermal expansion and photoinduced charge transfer. Finally, we identify areas for future research, ranging from the study of basic phenomena in solid-state photochemistry, to molecular and host matrix design, and the optimization of photoexcitation conditions. The ultimate realization of photon-fueled micromachines will likely involve advances spanning the disciplines of chemistry, physics and engineering.

Interactomics of Blebbistatin

Photoreactive molecules like aryl azides play important role in life sciences, as practical tools to achieve precisely timed covalent cross-links between ligands and targets. Since the azido group is small, stable and biologically inert, azido-modified aromatic drug molecules can keep their original pharmacological activity. By photoactivating of such modified molecules in vivo, both their strong and weak partners can be captured. Moreover, applying the azidated drug in a concentration range and utilizing proteomic tools the apparent binding constants of protein-ligand interactions can be determined.We have developed a new and simple technique to azidate aromatic drug molecules in an easy two step reaction. Using our method we have synthesized azidoblebbistatin which is a new derivative of blebbistatin, the most widely used myosin inhibitor. In the absence of UV irradiation azidoblebbistatin and blebbistatin exhibits identical inhibitory properties. Using UV light azidoblebbistatin can be covalently crosslinked to myosin whereas the unbound inhibitor molecules become inactive. Using Dictyostelium discoideum cell lysate we performed interactomic investigation to identify the previously unknown targets of blebbistatin utilizing the self- fluorescence of azidoblebbistatin. Since the crosslinking was performed applying increasing concentration of azidoblebbistatin, densitometry of the fluorescent spots resulting from gelelectrophoresis revealed the apparent binding constant of azidoblebbistatin. In case of myosin II it was the exact value as measured in in vitro tests. With this technique the strongest interactant was found to be myosin II (EC50=5 μM) while eight weak partners (EC50>30 μM) were also detected including vacuolar H+-ATPase (EC50=50 ± 31 μM), malate dehydrogenase (EC50=55 ± 17 μM) and elongation factor 1α (EC50>100 μM).

Adipogenic Differentiation of Individual Mesenchymal Stem Cell on Different Geometric Micropatterns

Micropatterned surfaces are very useful to control cell microenvironment and investigate the physical effects on cell function. In this study, poly(vinyl alcohol) (PVA) micropatterns on polystyrene cell-culture plates were prepared using UV photolithography. Cell adhesive polystyrene geometries of triangle, square, pentagon, hexagon, and circle were surrounded by cell nonadhesive PVA to manipulate cell shapes. These different geometries had the same small surface areas for cell spreading. Human mesenchymal stem cells (MSCs) were cultured on the micropatterned surface, and the effect of cell geometry on adipogenic differentiation was investigated. MSCs adhered to the geometric micropatterns and formed arrays of single cell with different shapes. The distribution patterns of actin filaments were similar among these cell shapes and remolded during adipogenesis. The adipogenic differentiation potential of MSCs was similar on the small size triangular, square, pentagonal, hexagonal, and circular geometries according to lipid vacuoles staining. This simple micropatterning technique using photoreactive molecules will be useful for creating micropatterns of arbitrary design on an organic surface, and cell functions can be directly and systematically compared on a single surface without external factors resulting from separate cell culture and coating method.

Quantum chemical calculations on solvation effects for selected photoreactive aromatic organic molecules of atmospheric relevance

The application of computational methods to studies in atmospheric chemistry is instrumental in understanding reaction mechanisms, dynamics, kinetics, particle nucleation and growth, and heterogeneous reactivity. There are a limited number of theoretical and experimental studies on the impact of surface photochemical reactions on water solubility and electronic properties of atmospheric aerosols, particularly those containing organic matter. We report computational results using density functional theory (DFT/B3LYP) on geometrical and electronic properties of selected aromatic organic molecules of interest to heterogeneous photochemistry in atmospheric aerosols. The impact of simulated explicit and implicit solvation on the aforementioned properties was examined for a number of organic compounds. Electronic absorption spectra calculated using time-dependent DFT with the B3LYP functional and 6-31G∗ basis set showed excellent agreement with experimental UV–visible spectra collected for these organic compounds. Results are discussed in light of the relative importance of implicit and explicit solvation for calculating the energies of electronic transitions, correlation between water solubility and hydrogen bonding between explicit water molecules and organic molecules.