Single-molecule spectroscopy studies of microenvironmental acidity in silicate thin films

Molecular design and architectonics towards film-based fluorescent sensing

The past few decades have witnessed encouraging progress in the development of high-performance film-based fluorescent sensors (FFSs) for detecting explosives, illicit drugs, chemical warfare agents (CWAs), and hazardous volatile organic chemicals (VOCs), among others. Several FFSs have transitioned from laboratory research to real-world applications, demonstrating their practical relevance. At the heart of FFS technology lies the sensing films, which play a crucial role in determining the analytes and the resulting signals. The selection of sensing fluorophores and the fabrication strategies employed in film construction are key factors that influence the fluorescence properties, active-layer structures, and overall sensing behaviors of these films. This review examines the progress and innovations in the research field of FFSs over the past two decades, focusing on advancements in fluorophore design and active-layer structural engineering. It underscores popular sensing fluorophore scaffolds and the dynamics of excited state processes. Additionally, it delves into six distinct categories of film fabrication technologies and strategies, providing insights into their advantages and limitations. This review further addresses important considerations such as photostability and substrate effects. Concluding with an overview of the field's challenges and prospects, it sheds light on the potential for further development in this burgeoning area.

Single Molecule Spectroscopy Studies of Acid-Base Chemical Gradients Using Nile Red as a Probe of Local Surface Acidity

Single molecule spectroscopy studies of local acidity along bifunctional acid-base gradients are reported. Gradients are prepared by directional vapor phase diffusion and subsequent reaction of 3-aminopropyl-trimethoxysilane with a uniform silica film. Gradient formation is confirmed by spectroscopic ellipsometry and by static water contact angle measurements. X-ray photoelectron spectroscopy is used to characterize the nitrogen content and degree of nitrogen protonation along the gradient. Nile Red is employed as the probe dye in single molecule spectroscopy studies of these gradients. While Nile Red is well-known for its solvent sensitivity, it is used here, for the first time, to sense the acid/base properties of the film in two-color wide-field fluorescence imaging experiments. The data reveal broad bimodal distributions of Nile Red emission spectra that vary along the gradient direction. The single molecule results are consistent with solution phase ensemble acid/base studies of the dye. The former reveal a gradual transition from a surface dominated by basic aminosilane sites at the high-amine end of the gradient to one dominated by acidic silanol sites at the low-amine end. The sub-diffraction-limited spatial resolution afforded by superlocalization of the single molecules reveals spatial correlations in the acid/base properties of the gradient over ∼200 nm distances. These studies provide data relevant to the use of aminosilane-modified silica in bifunctional, cooperative chemical catalysis.

Rhodols - synthesis, photophysical properties and applications as fluorescent probes

The formal replacement of one dialkylamino group in rhodamines with a hydroxyl group transforms them into rhodols. This apparently minor difference is not as small as one may think; rhodamines belong to the cyanine family whereas rhodols belong to merocyanines. Discovered in the late 19th century, rhodols have only very recently begun to gain momentum in the field of advanced fluorescence imaging. This is in part due to the increased understanding of their photophysical properties, and new methods of synthesis. Rationalization of how the nature and arrangement of polar substituents around the core affect the photophysical properties of rhodols is now possible. The emergence of so-called π-expanded and heteroatom-modified rhodols has also allowed their fluorescence to be bathochromically shifted into regions applicable for biological imaging. This review serves to outline applicable synthetic strategies for the synthesis of rhodols, and to highlight important structure-property relationships. In the first part of this Review, various synthetic methods leading to rhodols are presented, followed by structural considerations and an overview of photophysical properties. The second part of this review is entirely devoted to the applications of rhodols as fluorescent reporters in biological imaging.

Three-Dimensional pH Mapping within Model Hybrid Xerogel Thin Films

When xerogel films derived from carboxyethylsilanetriol (COE) and tetraethoxysilane (TEOS) or 3-aminopropyltriethoxysilane (APTES), n-octyltriethoxysilane (C8), and TEOS are formed on Al₂O₃ they exhibit chemically segregated domains with unique chemistries and topographies. These characteristics are important for marine antifouling. By using the ratiometric fluorescent probe 5 (and 6)-carboxy SNARF-1 (C.SNARF-1) in concert with confocal fluorescence microscopy, we determine the pH in three dimensions within these hybrid films. For the COE/TEOS film, 4-5 μm diameter dendritically shaped features form, and they extend ∼100 nm above the film base. These dendritic features are acidic (pH < 7) in comparison to the film base. Their average diameter decreases as we progress from the solution-film interface toward the film-Al₂O₃ interface. Planes located at the solution-film interface, film center, and film-Al₂O₃ interface exhibit acidic surface areas that are 20% below, 50% above, and 70% below the average COE mole fraction used to create the film. In the APTES/C8/TEOS films, 1-3 μm diameter mesa-shaped features form, and they extend up to 450 nm above the film base. These mesa features are basic (pH > 7) in comparison to the film base and are columnar in shape, extending without change in diameter throughout the entire film. From the solution-film interface the planes located within the first 3/4 of the film exhibit basic surface areas that are equivalent to the average APTES mole fraction used to create the film. However, as one approaches the film-Al₂O₃ interface, many new 100-200 nm basic subsurface regions appear. The basic surface area in those film planes within 400-500 nm of the film-Al₂O₃ interface are enriched in APTES by up to 500% above the average APTES mole fraction used to create the film.

Lipid-conjugated fluorescent pH sensors for monitoring pH changes in reconstituted membrane systems

Accurate real-time measurements of the dynamics of proton concentration gradients are crucial for detailed molecular studies of proton translocation by membrane-bound enzymes. To reduce complexity, these measurements are often carried out with purified, reconstituted enzyme systems. Yet the most paramount problem to detect pH changes in reconstituted systems is that soluble pH reporters leak out of the vesicle system during the reconstitution procedure. This requires loading of substantial amounts of pH-sensors into the lumen of unilamellar liposomes during reconstitution. Here, we report the synthesis and detailed characterisation of two lipid-linked pH sensors employing amine-reactive forms of seminaphthorhodafluors (SNARF®-1 dye) and rhodamine probes (pHrodo™ Red dye). Lipid-conjugation of both dyes allowed for efficient detergent-based reconstitution of these pH indicators into liposomes. Vesicle-embedded pHrodo™ displayed excellent photostability and an optimal pH-response between 4 and 7. The suitability of the lipid-linked pHrodo™ probe as a pH reporter was demonstrated by assaying the activity of a plant plasma membrane H(+)-ATPase (proton pump) reconstituted in proteoliposomes.

Single-molecule studies of acidity distributions in mesoporous aluminosilicate thin films

Solid acid catalysts are important for many petrochemical processes. The ensemble methods most often employed to characterize acid site properties in catalyst materials provide limited insights into their heterogeneity. Single-molecule (SM) fluorescence spectroscopic methods provide a valuable route to probing the properties of individual microenvironments. In this work, dual-color SM methods are adopted to study acidity distributions in mesoporous aluminosilicate (Al-Si) films prepared by the sol-gel method. The highly fluorescent pH-sensitive dye C-SNARF-1 was employed as a probe. The ratio of C-SNARF-1 emission in two bands centered at 580 and 640 nm provides an effective means to sense the pH of bulk solutions. In mesoporous thin films, SM emission data provide a measure of the effective pH of the microenvironment in which each molecule resides. SM emission data were obtained from mesoporous Al-Si films as a function of Al2O3 content for films ranging from 0% to 30% alumina. Histograms of the emission ratio reveal a broad distribution of acidity properties, with the film microenvironments becoming more acidic, on average, as the alumina content of the films increases. This work provides new insights into the distribution of Brønsted acidity in solid acids that cannot be obtained by conventional means.

Molecular design and synthesis of a pH independent and cell permeant fluorescent dye and its applications

A novel xanthene fluorescent dye with a combination of the desirable characters for fluorescent chemosensors and biomarkers including low molecular weight, water solubility, cell permeability, good biocompatibility, and strong tolerance to pH has been designed and synthesized.

Solvation dynamics and proton transfer in nanoconfined liquids

Nanoconfined liquids are of interest because of both their fundamental properties and their potential utility in an array of applications. The structure and dynamics of the liquid can be dramatically impacted by the geometrical constraints and the interactions with the interface. Understanding the molecular-level origins of these changes and how they are determined by the characteristics of the confining framework is the subject of ongoing experimental and theoretical studies. The progress and remaining challenges in these efforts are reviewed in the context of solvation dynamics and proton transfer reactions, processes that are strongly affected by nanoscale confinement.

Acidification of the oxygen scavenging system in single-molecule fluorescence studies: in situ sensing with a ratiometric dual-emission probe

For most of the single-molecule fluorescence studies to date, biomolecules of interest are labeled with small organic dyes which suffer from their limited photostability evidenced by blinking and photobleaching. An enzymatic oxygen scavenging system of glucose oxidase and catalase is widely used to improve the dye photostability but with the unfavorable side effect of producing gluconic acid. It is known that accumulation of this byproduct in solution can lead to considerable acidification, but the uncertainty in its severity under experimentally relevant conditions has been a long-standing area of concern due to the lack of a suitable assay. In this paper we report a fluorescence-based analytical assay for quantitatively assessing the acidification of oxygen scavenging systems in situ. By using a ratiometric, dual-emission dye, SNARF-1, we observed the presence and, for the first time, measured the severity of solution acidification due to the oxygen scavenging system for a number of conditions relevant to single-molecule studies. On the basis of the quantitative analysis of the acidification profile under these conditions, practical guidelines for optimizing the oxygen scavenging system are provided. This in situ assay should be applicable to a large variety of future single-molecule fluorescence studies.

Synthesis and characterization of pH sensitive carboxySNARF-1 nanoreactors

A rapid response dual wavelength emission pH sensor consisting of carboxySNARF-1 nanoreactors has been synthesized and shown to provide accurate pH measurements even in complex biological media, where the unprotected pH responsive dyes have failed. The carboxySNARF-1 nanoreactor is made of a calcium phosphate shell covering phosphatidylcholine liposomes filled with the dye. Its mean diameter is 150 nm with dynamic light scattering, the shell thickness is 5-7 nm with TEM, and it contains about 10 dyes/particle. The nanoreactor's response time to pH change nearly equals that of the dye in solution. Its pH titration curves at two different wavelengths are equivalent to those of the dye in solution and fluorescence intensity ratio dependent pH analysis is possible using the modified Henderson-Hasselbalch equation. However, the pH dependent fluorescence ratios of the dye in solution in the presence of plasma and albumin are distorted, and application of the Henderson-Hasselbalch equation is not possible. We have found that the distortions may be restored using cSNARF-1 nanoreactors and the pK(a) of the dye in the nanoreactor then equals that in solution. These results suggest that the interference to the dye for the pH analyses with the environmental molecules may be reduced or prohibited by usage of cSNARF-1 nanoreactors.

Experimentally and theoretically observed native pH shifts in a nanochannel array

Lab-on-a-chip (LOC) technology provides a powerful platform for simultaneous separation, purification, and identification of low concentration multicomponent mixtures. As the characteristic dimension of LOC devices decreases down to the nanoscale, the possibility of containing an entire lab on a single chip is becoming a reality. This research examines one of the unique physical characteristics of nanochannels, in which native pH shifts occur. As a result of the electrical double layer taking up a significant portion of a 100 nm wide nanochannel, electroneutrality no longer exists in the channel causing a radial pH gradient. This work describes experimentally observed pH shifts as a function of ionic strength using the fluorescent pH indicator 5-(and-6)-carboxy SNARF-1 and compares it to a model developed using Comsol Multiphysics. At low ionic strengths (approximately 3 mM) the mean pH shift is approximately 1 pH unit whereas at high ionic strengths (approximately 150 mM) the mean pH shift is reduced to 0.1 pH units. An independent analysis using fluorescein pH indicator is also presented supporting these findings. Two independent non-linear simulations coupling the Nernst-Planck equation describing transport in ionic solutions subjected to an electric field and Poisson's equation to describe the electric field as it relates to the charge distribution are solved using a finite element solver. In addition, the effects of chemical activities are considered in the simulations. The first numerical simulation is based on a surface zeta-potential which significantly underestimates the experimental results for most ionic strengths. A modified model assuming that SNARF and fluorescein molecules are able to diffuse into the hydrolyzed SiO2 phase, and in the case of the SNARF molecule, able to bind to neutral regions of the SiO2 phase agrees quantitatively with experimental results.

What can be learned from single molecule spectroscopy? Applications to sol-gel-derived silica materials

Single molecule spectroscopic methods are now being widely employed to probe the nanometer scale properties of sol-gel-derived silica materials. This article reviews a subset of the recent literature in this area and provides salient examples of the new information that can be obtained. The materials covered include inorganic and organically-modified silica, along with surfactant-templated mesoporous materials. Studies of molecule-matrix interactions based on ionic, hydrogen bonding and hydrophobic interactions are reviewed, highlighting the impacts of these interactions on mass transport phenomena. Quantitative investigations of molecular diffusion by single molecule tracking and fluorescence correlation spectroscopy are also covered, focusing on the characterization of anisotropic and hindered diffusion in mesoporous systems. Single molecule polarity studies are described and the new information that can be obtained from the resulting inhomogeneous distributions is discussed. Likewise, single molecule studies of silica acidity properties are reviewed, including observation of nanoscale buffering phenomena due to the chemistry of surface silanols. Finally, related single nanoparticle studies of macroporous silicas are also discussed.

Modified dual lifetime referencing method for simultaneous optical determination and sensing of two analytes

Simultaneous fluorometric sensing of two analytes becomes possible using a modified dual lifetime referencing (m-DLR) method. In this scheme, two luminescent indicators are needed that have overlapping absorption and emission spectra but largely different decay times. They are excited by a single light source, and both emissions are measured simultaneously. In the frequency domain m-DLR method, the phase of the short-lived fluorescence of a first indicator is referenced against that of the long-lived luminescence of the second indicator. The analytical information is obtained by measurement of the phase shifts at two modulation frequencies. The method is demonstrated to work for the case of dually sensing oxygen and carbon dioxide. It benefits from simple instrumentation and optical setup. The approach is perceived to be of wide applicability. Examples include (1) analysis of two luminescent analytes, (2) analytical determinations that make use of two probes, and (3) sensing of two species such as carbon dioxide and oxygen (as demonstrated here), or oxygen and chlorophyll, provided the luminophores meet the condition of having largely different decay times and overlapping absorption and emission spectra.

Glutamate optical biosensor based on the immobilization of glutamate dehydrogenase in titanium dioxide sol–gel matrix

A simple and novel titania sol-gel derived optical biosensor coupled with carboxy seminaphthorhodamine-1-dextran (SNARF-1-dextran) as the fluorescent dye was fabricated for the determination of glutamate in water and biological samples. The NADH-dependent glutamate dehydrogenase (GLDH) was trapped in titania sol-gel derived matrix prepared by vapor deposition method. In addition, scanning electron microscopy (SEM) and atomic force microscopy (AFM) were used to characterize the surface morphology of the spots. SEM and AFM images showed that the deposition of titania precursor at 27 degrees C for 6.5h was found to be suitable to form transparent titania sol-gel matrix to encapsulate GLDH and fluorescent probe. AFM images showed that the roughness of TiO(2) surface increased from 2.16 nm in the absence of GLDH and SNARF to 37.8 nm after the immobilization. The developed titania biosensor has good analytical performance with water samples. A dynamic range between 0.04 and 10mM with the detection limit of 5.5 microM were observed. The responses to glutamate in biological samples also showed good performances, and the dynamic range and detection limit were 0.02-10mM and 6.7 microM, respectively. High precision with relative standard deviations of 4.2 and 10.7% in water and biological samples, respectively, were also demonstrated. In addition, the biosensor showed a relatively high storage stability over more than 1 month. Results obtained in this study clearly demonstrate that this simple vapor deposition method can be successfully used to form transparent titania sol-gel film for the fabrication of glutamate biosensors that are suitable for optical detection of glutamate in water and biological samples.

Controlled bimolecular collisions allow sub-diffraction limited microscopy of lipid vesicles

The concentration and vesicle size-controlled collisions of single molecules with target biological assemblies allow sub-diffraction limited optical images to be obtained that are not subject to the usual photobleaching problems with single molecule experiments. For example, single molecules of the probe Nile Red in aqueous solution emit a burst of fluorescence when they collide with a 50 nm hydrophobic vesicle situated on the surface in the laser focus. The bimolecular kinetics of the bursts is defined by their on- and off-time distribution functions which depend on the concentration and diffusion of the probe and the vesicle size. The mean burst frequency changes much more sharply than does the fluorescence intensity when a vesicle is raster scanned through the laser focus. This sharpness allows the spatial resolution of two objects to be improved and separations less than the diffraction limited resolution of the conventional optical microscope to be measured. The principle of this method of trajectory time distribution optical microscopy (TTDOM) could be used in a far field optical microscopic system with a resolution of several nanometers.

Gaining insight into the nanoscale properties of sol-gel-derived silicate thin films by single-molecule spectroscopy

The application of single-molecule spectroscopic methods in studies of individual nanoscale environments within sol-gel-derived silicate thin films is reviewed. Representative examples of the experiments performed and results obtained in several studies from the authors' laboratories are given. Included are investigations of the static and dynamic polarity properties of organically modified silicate (ORMOSIL) films. The results of these studies point to nonrandom variations in the film properties, providing strong evidence for the formation of phase-separated organic- and inorganic-rich domains. Studies of single-molecule diffusion through the same films yield important evidence for the formation of liquidlike silicate oligomers that facilitate probe molecule diffusion. Finally, single-molecule studies of the local pH within individual film environments are discussed. Valuable information on the contributions of local materials' acidity variations to overall sample heterogeneity is obtained. The results of immersion studies indicate that certain molecular environments are inaccessible to external solutions over periods as long as a few hours. The article concludes with a discussion of possible future challenges in this research that may be addressed by new and existing single-molecule methods.