Single-Molecule Study of an Adsorbed Oligonucleotide Undergoing Both Lateral Diffusion and Strong Adsorption

Reaction-Initiated Single-Molecule Tracking of Mass Transfer in Core-Shell Mesoporous Silica Particles

Understanding the host-guest interactions in porous materials is of great importance in the field of separation science. Probing it at the single-molecule level uncovers the inter- and intraparticle inhomogeneity and establishes structure-property relationships for guiding the design of porous materials for better separation performance. In this work, we investigated the dynamics of host-guest interactions in core-shell mesoporous silica particles under in situ conditions by using a fluorogenic reaction-initiated single-molecule tracking (riSMT) approach. Taking advantage of the low fluorescence background, three-dimensional (3D) tracking of the dynamics of the molecules inside the mesoporous silica pore was achieved with high spatial precision. Compared to the commonly used two-dimensional (2D) tracking method, the 3D tracking results show that the diffusion coefficients of the molecules are three times larger on average. Using riSMT, we quantitatively analyzed the mass transfer of probe molecules in the mesoporous silica pore, including the fraction of adsorption versus diffusion, diffusion coefficients, and residence time. Large interparticle inhomogeneity was revealed and is expected to contribute to the peak broadening for separation application at the ensemble level. We further investigated the impact of electrostatic interaction on the mass transfer of molecules in the mesoporous silica pore and discovered that the primary effect is on the fraction rather than their diffusion rates of resorufin molecules undergoing diffusion.

Adsorption and desorption mechanisms on graphene oxide nanosheets: Kinetics and tuning

A knowledge of the adsorption and desorption behavior of sorbates on surface adsorptive site (SAS) is the key to optimizing the chemical reactivity of catalysts. However, direct identification of the chemical reactivity of SASs is still a challenge due to the limitations of characterization techniques. Here, we present a new pathway to determine the kinetics of adsorption/desorption on SASs of graphene oxide (GO) based on total internal reflectance fluorescence microscopy. The switching on and off of the fluorescent signal of SAS lit by carbon dots (CDs) was used to trace the adsorption process and desorption process. We find that sodium pyrophosphate (PPi) could increase the adsorption equilibrium of CDs thermodynamically and promote the substrate-assisted desorption pathway kinetically. At the single turnover level, it was disclosed that the species that can promote desorption may also be an adsorption promoter. Such discovery provides significant guidance for improving the chemical reactivity of the heterogeneous catalyst.

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The kinetics of adsorption and desorption process were revealed, respectively, by monitoring a fluorogenic process of carbon dots on the surface of graphene oxides at the single turnover level

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By regulating the equilibrium of adsorption and desorption, a mechanism for the simultaneous promotion of adsorption and desorption has been discovered

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A desorption accelerator could play a satisfactory double action, i.e., adsorption promoter on thermodynamics and desorption promoter on kinetics

A new metric for relating macroscopic chromatograms to microscopic surface dynamics: the distribution function ratio (DFR)

Heterogeneous stationary phase chemistry causes chromatographic tailing that lowers separation efficiency and complicates optimizing mobile phase conditions. Model-free metrics are attractive for assessing optimal separation conditions due to the low quantity of information required, but often do not reveal underlying mechanisms that cause tailing, for example, heterogeneous retention modes. We report a new metric, which we call the Distribution Function Ratio (DFR), based on a graphical comparison between the chromatogram and Gaussian cumulative distribution functions, achieving correspondence to ground truth surface dynamics with a single chromatogram. Using a Monte Carlo framework, we show that the DFR can predict the prevalence of heterogeneous retention modes with high precision when the relative desorption rate between modes is known, as in during surface dynamics experiments. Ground truth comparisons reveal that the DFR outperforms both the asymmetry factor and skewness by yielding a one-to-one correspondence with heterogeneous retention mode prevalence over a broad range of experimentally realistic values. Perhaps of more value, we illustrate that the DFR, when combined with the asymmetry factor and skewness, can estimate microscopic surface dynamics, providing valuable insights into surface chemistry using existing chromatographic instrumentation. Connecting ensemble results to microscopic quantities through the lens of simulation establishes a new chemistry-driven route to measuring and advancing separations.

Single molecule fluorescence imaging of nanoconfinement in porous materials

This review covers recent progress in using single molecule fluorescence microscopy imaging to understand the nanoconfinement in porous materials. The single molecule approach unveils the static and dynamic heterogeneities from seemingly equal molecules by removing the ensemble averaging effect. Physicochemical processes including mass transport, surface adsorption/desorption, and chemical conversions within the confined space inside porous materials have been studied at nanometer spatial resolution, at the single nanopore level, with millisecond temporal resolution, and under real chemical reaction conditions. Understanding these physicochemical processes provides the ability to quantitatively measure the inhomogeneities of nanoconfinement effects from the confining properties, including morphologies, spatial arrangement, and trapping domains. Prospects and limitations of current single molecule imaging studies on nanoconfinement are also discussed.

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.

Molecular orientation and its influence on autocorrelation amplitudes in single-molecule imaging experiments

The concentration dependence of autocorrelation amplitudes obtained from orientationally fixed single molecules is explored using theory, simulation, and experimental results. Autocorrelation amplitudes obtained under such circumstances are shown to be approximately 2-fold larger than predicted in previous studies (Koppel, D. E. Phys. Rev. A 1974, 10, 1938-1945 and citing references), which frequently assume polarization-independent excitation and detection. A detailed derivation of the autocorrelation amplitude expected under conditions frequently employed in single-molecule experiments is given. Simulated and experimental single-molecule image data obtained from samples incorporating fixed single molecules are used to verify the correctness of the model. These results are compared to both simulated and experimental time transient data in which the molecules exhibit predominantly fast rotational reorientation and to which previously reported models apply. The experimental results employed are obtained from dye-doped mesoporous silica thin films studied at different levels of hydration. The theory and results obtained are of importance to the determination of molecular concentrations from single-molecule image and time transient autocorrelation data, in situations where the molecules exhibit permanent or reversible adsorption at fixed orientations in or on thin-film materials.

Enhanced fluorescence of Cy5-labeled DNA tethered to silver island films: fluorescence images and time-resolved studies using single-molecule spectroscopy

Methods that increase the total emission per fluorophore would provide increased sensitivity and a wider dynamic range for chemical analysis, medical diagnostics, and in vivo molecular imaging. The use of fluorophore-metal interactions has the potential to dramatically increase the detectability of single fluorophores for bioanalytical monitoring. The fabrication and single-molecule analysis of fluorophore-labeled DNA molecules tethered to silver island films are described in this article. The single-molecule spectroscopic method reveals some insightful information on the behaviors of single molecules, rather than an ensemble of molecules. Analysis of fluorescence images, intensity profiles, total emitted photons, and lifetime distributions reveals some of sample heterogeneities. Investigations of time-dependent emission characteristics of single molecules indicate that the total number of emitted photons on the silvered surface is more than 10 times greater than on free labeled DNA molecules on a glass substrate. In addition, time-correlated single-photon counting results reveal the reduced lifetimes of single molecules tethered to silver island films.

Enhanced fluorescence of Cy5-labeled oligonucleotides near silver island films: a distance effect study using single molecule spectroscopy

We investigated fluorescence enhancements and lifetime reductions of Cy5 probe molecules at various distances from the deposited silver island film surface using single molecule spectroscopic methods. The proximity of fluorophore molecules to the surface was controlled by alternating layers of biotinylated bovine serum albumin (BSA-biotin) and avidin, followed by binding of Cy5-labeled oligonucleotides to the top of a BSA-biotin layer structure. We observed dramatically varied brightness of fluorophores with distances from metal structures as well with reduced blinking in the presence of silver island films. In addition, distributions of fluorescence lifetimes and apparent emission intensities from individual molecules indicate an inhomogeneous nature of local matrix surface near metallic nanostructures. These studies illustrate the exclusive information that is otherwise hidden in ensemble measurements.

Single Molecule Spectroscopy Studies of Diffusion in Mesoporous Silica Thin Films

Single molecule spectroscopy is applied in studies of diffusion and surface adsorption in sol-gel-derived mesoporous silica thin films. Mesoporous films are obtained by spin casting surfactant-templated sols onto glass substrates. Small-angle X-ray diffraction results are consistent with hexagonally ordered mesophases in as-synthesized (i.e., surfactant-containing) films. Upon calcination, a 30% contraction and disordering of these structures occurs. Nile Red is used as a fluorescent probe of both the as-synthesized and calcined films. It is loaded into the samples at subnanomolar levels either prior to spin casting or after calcination. Fluorescence imaging and single-point fluorescence time transients show the dye molecules to be relatively mobile in the as-synthesized samples. In contrast, the molecules appear entrapped at fixed locations in dry calcined films. In calcined films rehydrated under high humidity conditions, the Nile Red molecules again become mobile. Time transients obtained from the as-synthesized and rehydrated samples provide clear evidence for frequent reversible adsorption of the dye to the silica surfaces. Autocorrelations of the time transients provide quantitative data on the mean diffusion coefficients (D = 2.4 x 10(-10) and 2.6 x 10(-10) cm2/s) and mean desorption times (1/k = 25 and 40 s) for the as-synthesized and rehydrated films, respectively. The results prove both water and surfactant play important roles in governing matrix interactions and mass transport.

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.

Real-Time Dipole Orientational Imaging as a Probe of Ligand−Protein Interactions

Single-molecule orientational imaging using total internal reflection fluorescence microscopy has been employed to investigate the dynamics of a protein-ligand system. Emission patterns from single tetramethylrhodamine (TMR)-biocytin molecules bound to streptavidin show that the TMR dipole adopts a limited number of favored orientations. The angular trajectories of individual dipoles exhibit remarkably similar patterns that are characteristic of single TMR molecules interacting with a relatively homogeneous population of nanoenvironments. Analysis of the polar and azimuthal angle distributions reveals a tendency for the dipole to assume three primary and two secondary orientations. Autocorrelation analysis of the dipole trajectories shows a predominantly bimodal behavior in the reorientation rates with the slow and fast components corresponding to the primary and secondary orientations, respectively. A number of mechanisms by which the observed orientations might be stabilized have been considered, in particular specific interactions between the zwitterionic TMR probe and charged residues on the streptavidin surface. Variations in the reorientation rates have been discussed in terms of local thermal fluctuations in the protein.

Single-Molecule Studies of Diffusion by Oligomer-Bound Dyes in Organically Modified Sol−Gel-Derived Silicate Films

Single-molecule fluorescence spectroscopy is used to study dye diffusion within organically modified silicate (ORMOSIL) films. ORMOSIL films are prepared from sols containing tetraethoxysilane and isobutyltrimethoxysilane in 2:1 and 1:9 molar ratios. Nile red and a new silanized form of nile red that can be covalently attached to the silicate matrix are used as fluorescent probe molecules. The number and rate of single molecules diffusing through these films increases dramatically with increasing film organic content. Autocorrelation of the fluorescence images yields a quantitative measure of the relative populations of fixed and diffusing species. Surprisingly, both "free" and silicate-bound nile red exhibit relatively facile translational motions. Single-molecule/single-point fluorescence correlation spectroscopy (FCS) is used to measure the dye diffusion coefficients in submicrometer-scale film regions. The most common diffusion coefficients for "free" and silicate-bound nile red molecules in the 1:9 films are 3.9 x 10(-10) and 1.6 x 10(-10) cm(2)/s, respectively. The unexpectedly rapid diffusion of silicate-bound nile red is attributed to the presence of liquidlike silicate oligomers in the films. A lower bound for the molecular weight of the oligomers is estimated at 2900. Bulk solution-phase FCS experiments performed on "free" and silicate-bound nile red species extracted into chloroform solutions provide valuable support for these conclusions. Comparison of the results derived from experimental and simulated time transients indicates film heterogeneity occurs on sub-100-nm-length scales and likely results from the presence of inorganic- and organic-rich domains.

The Vroman Effect: A Molecular Level Description of Fibrinogen Displacement

The molecular level details of the displacement of surface adsorbed fibrinogen from silica substrates were studied by atomic force microscopy, immunochemical assays, fluorescence microscopy, and vibrational sum frequency spectroscopy. The results showed that human plasma fibrinogen (HPF) can be readily displaced from the interface by other plasma proteins near neutral pH because the positively charged alpha C domains on HPF sit between the rest of the macromolecule and the underlying surface. The alpha C domains make weak electrostatic contact with the substrate, which is manifest by a high degree of alignment of Lys and Arg residues. Upon cycling through acidic pH, however, the alpha C domains are irreversibly removed from this position and the rest of the macromolecule is free to engage in stronger hydrogen bonding, van der Waals, and hydrophobic interactions with the surface. This results in a 170-fold decrease in the rate at which HPF can be displaced from the interface by other proteins in human plasma.

Single-Molecule Fluorescence Trajectories for Investigating Molecular Transport in Thin Silica Sol−Gel Films

Single-molecule fluorescence tracking has been used to examine diffusion of small molecules in sol-gel films in order to identify spatial heterogeneity in the structure and molecular diffusivities for different regions of the film. Fluorescence intensity profiles from single molecules are fit to a two-dimensional Gaussian function to determine their x,y positions with subpixel resolution. Scatter plots and histograms of molecular step sizes indicate that the trajectories conform to the predictions of a two-dimensional random walk. The mean-square step size is shown to be an unbiased estimate of the variance of the step-size probability distribution and a valid statistic for determining the diffusion coefficient from a molecular trajectory. The diffusion coefficients measured for different molecules are subjected to an F test, which showed that the sol-gel film exhibits spatial variation in the diffusion coefficient on a micrometer-length scale. The spatial variation in diffusivities is a measure of structural heterogeneity of these films.

Quantitative dosing of surfaces with fluorescent molecules: characterization of fractional monolayer coverages by counting single molecules

Quantitative deposition of dye molecules onto a substrate has been achieved at very low surface concentrations, in the range of 5 x 10(-8) - 1 x 10(-6) monolayer, using the technique of controlled substrate withdrawal from solution. These small surface populations were determined with high (>96%) efficiency by single-molecule counting using an epi-illumination, fluorescence microscope with charge-coupled device detector. The fluorescence imaging resolution (3sigma) is 0.78 microm; over a uniform excitation area of 67 x 67 microm2, a large number (>7,500) of spatially resolved channels are available for counting individual molecules. At low coverages, the number density of fluorescence spots on the surface agrees with the expected surface concentration of molecules, based on the concentration of dye in solution and the solution film thickness predicted from theory. When the surface density of molecules is high enough that fluorescence spot overlap is likely to occur within the optical resolution of the instrument, the observed fewer number of spots can be corrected for overlap through a site occupation model based on Poisson statistics.