Bioluminescence - The Vibrant Glow of Nature and its Chemical Mechanisms.

Bioluminescence, the mesmerizing natural phenomenon where living organisms produce light through chemical reactions, has long captivated scientists and laypersons alike, offering a rich tapestry of insights into biological function, ecology, evolution as well as the underlying chemistry. This comprehensive introductory review systematically explores the phenomenon of bioluminescence, addressing its historical context, geographic dispersion, and ecological significance with a focus on their chemical mechanisms. Our examination begins with terrestrial bioluminescence, discussing organisms from different habitats. We analyze thefireflies of Central Europe's meadows and the fungi in the Atlantic rainforest of Brazil. Additionally, we inspect bioluminescent species in New Zealand, specifically river-dwelling snails and mosquito larvae found in Waitomo Caves. Our exploration concludes in the Siberian Steppes, highlighting the area's luminescent insects and annelids. Transitioning to the marine realm, the second part of this review examines marine bioluminescent organisms. We explore this phenomenon in deep-sea jellyfish and their role in the ecosystem. We then move to Toyama Bay, Japan, where seasonal bioluminescence of dinoflagellates and ostracods present a unique case study. We also delve into the bacterial world, discussing how bioluminescent bacteria contribute to symbiotic relationships. For each organism, we contextualize its bioluminescence, providing details about its discovery, ecological function, and geographical distribution. A special focus lies on the examination of the underlying chemical mechanisms that enables these biological light displays. Concluding this review, we present a series of practical bioluminescence and chemiluminescence experiments, providing a resource for educational demonstrations and student research projects. Our goal with this review is to provide a summary of bioluminescence across the diverse ecological contexts, contributing to the broader understanding of this unique biological phenomenon and its chemical mechanisms serving researchers new to the field, educators and students alike.

Spectrochemistry of Firefly Bioluminescence.

The chemical reactions underlying the emission of light in fireflies and other bioluminescent beetles are some of the most thoroughly studied processes by scientists worldwide. Despite these remarkable efforts, fierce academic arguments continue around even some of the most fundamental aspects of the reaction mechanism behind the beetle bioluminescence. In an attempt to reach a consensus, we made an exhaustive search of the available literature and compiled the key discoveries on the fluorescence and chemiluminescence spectrochemistry of the emitting molecule, the firefly oxyluciferin, and its chemical analogues reported over the past 50+ years. The factors that affect the light emission, including intermolecular interactions, solvent polarity, and electronic effects, were analyzed in the context of both the reaction mechanism and the different colors of light emitted by different luciferases. The collective data points toward a combined emission of multiple coexistent forms of oxyluciferin as the most probable explanation for the variation in color of the emitted light. We also highlight realistic research directions to eventually address some of the remaining questions related to firefly bioluminescence. It is our hope that this extensive compilation of data and detailed analysis will not only consolidate the existing body of knowledge on this important phenomenon but will also aid in reaching a wider consensus on some of the mechanistic details of firefly bioluminescence.

Natural Product Isolation of the Extract of Cleome rupicola Fruits Exhibiting Antioxidant Activity.

Cataracts are the leading cause of blindness worldwide, however, there is currently no drug-based treatment. Plants that exhibit antioxidant properties have shown promising anticataract effects, likely because they supplement the activity of glutathione, the major antioxidant in lens cells. An extract of Cleome rupicola, a desert plant found in the United Arab Emirates, has traditionally been used to treat cataracts. Phytochemical screening of the aqueous extract established the presence of flavonoids, tannins, steroid derivatives, and reducing sugars. Fractioning of extracts from the fruits using high-performance liquid chromatography (HPLC) yielded the isolation of the anthelmintic compound cleomin, and its structure was confirmed using mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy.

Cracking under Internal Pressure: Photodynamic Behavior of Vinyl Azide Crystals through N2 Release.

When exposed to UV light, single crystals of the vinyl azides 3-azido-1-phenylpropenone (1a), 3-azido-1-(4-methoxyphenyl)propenone (1b), and 3-azido-1-(4-chlorophenyl)propenone (1c) exhibit dramatic mechanical effects by cracking or bending with the release of N2. Mechanistic studies using laser flash photolysis, supported by quantum mechanical calculations, show that each of the vinyl azides degrades through a vinylnitrene intermediate. However, despite having very similar crystal packing motifs, the three compounds exhibit distinct photomechanical responses in bulk crystals. While the crystals of 1a delaminate and release gaseous N2 indiscriminately under paraffin oil, the crystals of 1b and 1c visibly expand, bend, and fracture, mainly along specific crystallographic faces, before releasing N2. The photochemical analysis suggests that the observed expansion is due to internal pressure exerted by the gaseous product in the crystal lattices of these materials. Lattice energy calculations, supported by nanoindentation experiments, show significant differences in the respective lattice energies. The calculations identify critical features in the crystal structures of 1b and 1c where elastic energy accumulates during gas release, which correspond to the direction of the observed cracks. This study highlights the hitherto untapped potential of photochemical gas release to elicit a photomechanical response and motility of photoreactive molecular crystals.

Chemi- and Bioluminescence of Cyclic Peroxides.

Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.

Mechanically Assisted Bioluminescence with Natural Luciferase.

Mechanochemical analogues have recently been established for several enzymatic reactions, but they require periodic interruption of the reaction for sampling, dissolution, and (bio)chemical analysis to monitor their progress. By applying a mechanochemical procedure to induce bioluminescence analogous to that used by the marine ostracod Cypridina (Vargula) hilgendorfii, here we demonstrate that the light emitted by a bioluminescent reaction can be used to directly monitor the progress of a mechanoenzymatic reaction without sampling. Mechanical treatment of Cypridina luciferase with luciferin generates bright blue light which can be readily detected and analyzed spectroscopically. This mechanically assisted bioluminescence proceeds through a mechanism identical to that of bioluminescence in solution, but has higher activation energy due to being diffusion-controlled in the viscous matrix. The results suggest that luciferases could be used as light-emissive reporters of mechanoenzymatic reactions.

Signatures of Quark-Hadron Phase Transitions in General-Relativistic Neutron-Star Mergers.

Merging binaries of neutron-stars are not only strong sources of gravitational waves, but also have the potential of revealing states of matter at densities and temperatures not accessible in laboratories. A crucial and long-standing question in this context is whether quarks are deconfined as a result of the dramatic increase in density and temperature following the merger. We present the first fully general-relativistic simulations of merging neutron-stars including quarks at finite temperatures that can be switched off consistently in the equation of state. Within our approach, we can determine clearly what signatures a quark-hadron phase transition would leave in the gravitational-wave signal. We show that if after the merger the conditions are met for a phase transition to take place at several times nuclear saturation density, they would lead to a postmerger signal considerably different from the one expected from the inspiral, that can only probe the hadronic part of the equations of state, and to an anticipated collapse of the merged object. We also show that the phase transition leads to a very hot and dense quark core that, when it collapses to a black hole, produces a ringdown signal different from the hadronic one. Finally, in analogy with what is done in heavy-ion collisions, we use the evolution of the temperature and density in the merger remnant to illustrate the properties of the phase transition in a QCD phase diagram.

Reversible Multicolor Photochromism of Dihydroazulene Crystals.

The photochemical conversion of 1,8a-dihydroazulene-1,1-dicarbonitrile (DHA) to vinylheptafulvene (VHF) is a positive T-type photoswitch that is well understood in solution, but has not been explored in the solid state. Upon excitation with UV light, DHA is converted into VHF in the solid state, with a distinct color change from yellow to deep-red, and retention of crystallinity. The structure of the ring-opened product was assigned to syn-VHF using variable-temperature infrared spectroscopy, and determined by X-ray photodiffraction in a crystal enriched with the product by two-photon excitation. A radical pathway becomes an observable photoreaction channel at low temperatures, and includes a strongly colored, short-lived diradical intermediate.

Dual-Mode Light Transduction through a Plastically Bendable Organic Crystal as an Optical Waveguide.

An anthracene derivative, 9,10-dicyanoanthracene, crystallizes as fluorescent needle-like single crystals that can be readily plastically bent in two directions. Spatially resolved photoluminescence analysis revealed that this material has robust optoelectronic properties that are preserved upon extreme crystal deformation. The highly flexible crystals were successfully tested as efficient switchable optical waveguiding elements for both active and passive light transduction, and the mode of operation depends on the wavelength of the incident light. This prototypical dual-mode organic optical crystalline fiber brings mechanically compliant molecular organic crystals closer to applications as novel light-transducing media for wireless transfer of information in all-organic micro-optoelectronic devices.

Turning on Solid-State Fluorescence with Light.

A bioinspired fluorophore that is analogous to the substrate in the bioluminescence of fireflies was prepared and reacts when exposed to weak blue LED light. Upon excitation, this material is photodecarboxylated with a nearly 81-fold enhancement of the solid-state emission, the fluorescence quantum yield of the product in solution is approximately 90 %, and violent disintegrative effects occur as a result of the release of carbon dioxide. Crystallographic and computational results, together with global spectral analysis of the kinetics, confirmed that most of the emission observed in the decay-associated spectra is intrinsic to the product molecule, with only a minor contribution from an excimer through π-π stacking of the molecules in the crystal.

From Highly Fluorescent Donors to Strongly Absorbing Acceptors: The Tunable Properties of Fluorubines.

The synthesis and characterization of three novel fluorubine derivatives is reported via three to four simple reaction steps with isolatable intermediates. The functional dyes are characterized by their strong absorption peaks in the visible region and their high fluorescence quantum yields. A significant and useful feature is that the properties can be tuned over a wide range by changing the pH. Transformation of the dyes into protonated amidinium salts leads to narrower band gaps and to drastically lower LUMO energies. Further reduction of the pH results in the doubly protonated species with a high electron-deficiency and LUMO energies of -4.8 eV, bathochromic shifts, and a strong intensity increase of up to ε = 120 000 M-1 cm-1.

Mechanistic investigations of the 2-coumaranone chemiluminescence.

2-Coumaranones are evolving as a new, efficient, versatile, and synthetically accessible platform for the next generation chemiluminescent probes. Despite the favorable quantum yields, the exact mechanism of their chemiluminescence remains elusive. Here, we analyze the details of the mechanism of the 2-coumaranone chemiluminescence using a combination of experimental and computational methods. By using EPR spectroscopy we show that superoxide radical anions are involved in the reactions, in support of the hypothesis that the mechanism includes a single electron transfer step. The decomposition of the high-energy intermediate, 1,2-dioxetanone, is described in the ground state and in the first three excited singlet states, and indicates that there is at least one conical intersection, which is crucial for generation of excited-state molecules. A peroxy anion that is generated was found to be able to undergo a side reaction that leads to the same (isolated) product as in the light-generating reaction. These results demonstrate the applicability of 2-coumaranones as a model system for several bioluminescence reactions and may lead to the design of new 2-coumaranone derivatives with superior emission characteristics for bioanalytical applications.

π-Extension of a 4-ethoxy-1,3-thiazole via aryl alkyne cross coupling: synthesis and exploration of the electronic structure.

A series of four donor aryl alkynyl substituted thiazole derivatives 3a-d and three similar aryl donor-acceptor systems 6a-c have been synthesized. All compounds bear different electron-donating groups in the 5-position of the thiazole core. The influence of both electron donor strength and the additional phenylethynyl unit on photophysical properties, i.e. UV/Vis absorption, fluorescence emission and fluorescence lifetime, has been evaluated. Additionally, theoretical calculations have been performed at the CAM-B3LYP/6-31+G(d,p) level and good agreement with the experimental data has been achieved. The new derivatives synthesized via palladium catalyzed cross coupling are characterised by moderately strong emission between 474 and 538 nm (ΦF = 0.35-0.39) and Stokes' shifts ranging from 0.54 to 0.79 eV (4392-6351 cm(-1)). The smaller chromophores of type 6 exhibit modest to high fluorescence emission (ΦF = 0.45-0.76) between 470 and 529 nm and their Stokes' shifts range from 0.59 to 0.65 eV (4765-5251 cm(-1)).

Evidence supporting a 1,2-dioxetanone as an intermediate in the benzofuran-2(3H)-one chemiluminescence.

The mechanism of the chemiluminescent reaction of ethyl (5-fluoro-2-oxo-2,3-dihydrobenzofuran-3-yl) carbamate (a 2-coumaranone derivative) with a base and molecular oxygen was investigated. New evidence from the reaction kinetics and absorption/emission profiles was obtained, supporting the existence of a 1,2-dioxetanone as an intermediate: (i) its characteristic activation parameters (ΔH(≠) = 7.2 ± 0.1 kcal mol(-1); ΔS(≠) = -45 ± 5 cal K(-1) mol(-1)) indicating a high degree of thermal instability and (ii) its bimolecular decomposition rate constant for the reaction with perylene. The newly developed methodology has been shown to be suitable for determining the reactivity of such thermally unstable peroxides, which are very difficult to prepare and isolate, using this alternative approach of in situ generation of a 1,2-dioxetanone.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

A modified Hartmann-Shack aberrometer for measuring stray light in the anterior segment of the human eye.

PURPOSE: To examine the use of a modified Hartmann-Shack wave front aberrometer (WASCA; Carl Zeiss Meditec AG, Germany) to measure objective stray light caused by forward light scatter from the anterior segment of the human eye. SETTING: HELIOS Klinikum Erfurt/Institute of Biomedical Engineering and Informatics, Ilmenau University of Technology, Germany. METHOD: Scatter parameters, including the Michelson contrast and cross-sectional area at half height (CAHM) were examined in Hartmann-Shack images from ten subjects with a cataract in one eye and an intraocular lens (IOL) in the other. The parameters were compared between each eye. Light scatter was then measured in 40 healthy subjects (age range, 23-75 years) with spherical ametropia ranging from -0.25 to 0.25 diopters. The subjects were divided into three age groups; 23-35, 36-50, and 51-75 years. Light scatter was also measured using four alternative methods. RESULTS: CAHM and contrast were significantly different between the eyes with the cataract and the IOL (P = 0.007 and P = 0.004, respectively). CAHM (r = 0.557, P < 0.001) and contrast (r = -0.467, P < 0.001) were both significantly correlated with age. There were significant differences in CAHM and contrast between the age groups. CONCLUSION: The modified wave front aberrometer can be used to measure stray light, although its diagnostic sensitivity in individual patients must be improved.

Three-Dimensional Light Field Fundus Imaging: Automatic Determination of Diagnostically Relevant Optic Nerve Head Parameters.

Purpose: Morphological changes to the optic nerve head (ONH) can be detected at the early stages of glaucoma. Three-dimensional imaging and analysis may aid in the diagnosis. Light field (LF) fundus cameras can generate three-dimensional (3D) images of optic disc topography from a single shot and are less susceptible to motion artifacts. Here, we introduce a processing method to determine diagnostically relevant ONH parameters automatically and present the results of a subject study performed to validate this method. Methods: The ONHs of 17 healthy subjects were examined and images were acquired with both an LF fundus camera and by optical coherence tomography (OCT). The LF data were analyzed with a novel algorithm and compared with the results of the OCT study. Depth information was reconstructed, and a model with radial basis functions was used for processing of the 3D point cloud and to provide a finite surface. The peripapillary rising and falling edges were evaluated to determine optic disc and cup contours and finally calculate the parameters. Results: Nine of the 17 subjects exhibited prominent optic cups. The contours and ONH parameters determined by an analysis of LF 3D imaging largely agreed with the data obtained from OCT. The median disc areas, cup areas, and cup depths differed by 0.17 mm², -0.04 mm², and -0.07 mm, respectively. Conclusions: The findings presented here suggest the possibility of using LF data to evaluate the ONH. Translational Relevance: LF data can be used to determine geometric parameters of the ONH and thus may be suitable for future use in glaucoma diagnostics.

Analysis of optical side-effects of fs-laser therapy in human presbyopic lens simulated with modified contact lenses.

BACKGROUND: In a single-blinded study, optical side-effects of a potential femtosecond (fs)-laser therapy in presbyopic human lenses were tested. Simulation of this therapy was carried out by applying fs-laser patterns into standard contact lenses (CL). METHODS: In the first part of the study, the influence of the numerical aperture on optical side-effects was investigated by comparing a typical fs-LASIK configuration to a fs-presbyopia treatment (n = 11). The second part focused on a possible improvement of visual performance by comparing a regular grid pattern to a randomly chosen spacing of the laser spots (n = 16). Visual acuity was measured with ETDRS charts, contrast sensitivity with F.A.C.T. charts and mesopic vision with Mesotest II. Forward scattered light was measured with the C-Quant (both instruments: Oculus Optikgeräte GmbH, Germany). A questionnaire detected subjective quality of vision. Differences between laser-treated and untreated CL and among the modifications were analyzed. RESULTS: The laser-treated and standard CL indicated no significant difference in visual acuity, contrast sensitivity and mesopic vision without glare. While wearing modified lenses with a regular grid, quality of vision decreased significantly by means of mesopic vision with glare and subjective straylight. These modifications also caused an impairment of subjective quality of vision. In contrast, there was no significant difference between the random pattern and standard CL. CONCLUSION: The increase of optical side-effects was reproducibly dependent on the geometry of the laser-structure. A randomized grid induced the least limitation. The study results are useful for planning possible laser-patterns in fs-laser therapy of the presbyopic lens.

3D retinal imaging and measurement using light field technology.

SIGNIFICANCE: Light-field fundus photography has the potential to be a new milestone in ophthalmology. Up-to-date publications show only unsatisfactory image quality, preventing the use of depth measurements. We show that good image quality and, consequently, reliable depth measurements are possible, and we investigate the current challenges of this novel technology. AIM: We investigated whether light field (LF) imaging of the retina provides depth information, on which structures the depth is estimated, which illumination wavelength should be used, whether deeper layers are measurable, and what kinds of artifacts occur. APPROACH: The technical setup, a mydriatic fundus camera with an LF imager, and depth estimation were validated by an eye model and in vivo measurements of three healthy subjects and three subjects with suspected glaucoma. Comparisons between subjects and the corresponding optical coherence tomography (OCT) measurements were used for verification of the depth estimation. RESULTS: This LF setup allowed for three-dimensional one-shot imaging and depth estimation of the optic disc with green light. In addition, a linear relationship was found between the depth estimates of the OCT and those of the setup developed here. This result is supported by the eye model study. Deeper layers were not measurable. CONCLUSIONS: If image artifacts can be handled, LF technology has the potential to help diagnose and monitor glaucoma risk at an early stage through a rapid, cost-effective one-shot technology.