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The presence of so-called reversible and irreversible protein adsorption on solid surfaces is well documented in the literature and represents the basis for the development of nanoparticles and implant materials to control interactions in physiological environments. Here, using a series of complementary single-molecule tracking approaches appropriate for different timescales, we show that protein desorption kinetics is much more complex than the traditional reversible-irreversible binary picture. Instead, we find that the surface residence time distribution of adsorbed proteins transitions from power law to exponential behavior when measured over a large range of timescales (10

Liquid crystal elastomers (LCEs) are stimuli-responsive materials that undergo large shape transformations after undergoing an order-disorder transition. While shape reconfigurations in LCEs are predominantly triggered by heat, there is a considerable interest in developing highly specific triggers that work at room temperature. Herein, we report the fabrication of biocatalytic LCEs that respond to the presence of urea by covalently immobilizing urease within chemically responsive LCE networks. The hydrogen-bonded LCEs developed in this work exhibited contractile strains of up to 36% upon exposure to a base. Notably, the generation of ammonia by immobilized urease triggered a disruption in the supramolecular network and a large reduction of liquid crystalline order in the films when the LCEs were exposed to urea. This reduction in order was macroscopically translated into a strain response that could be modulated by changing the concentration of urea or exposure time to the substrate. Local control of the mechanical response of the LCE was realized by spatially patterning the enzyme on the surface of the films. Subsequent exposure of enzymatically patterned LCE to urea-triggered 3D shape transformations into a curl, arch, or accordion-like structure, depending on the motif patterned on the film surface. Furthermore, we showed that the presence of salt was critical to prevent bridging of the network by the presence of ammonium ions, thereby enabling such macroscopic 3D shape changes. The large actuation potential of LCEs and the ability to translate the biocatalytic activity of enzymes to macroscopic 3D shape transformations could enable use in applications ranging from cell culture, medicine, or antifouling.

The facilitated surface diffusion of transiently adsorbing molecules in a planar confined microenvironment (i.e., slit-like confinement) is highly relevant to biological phenomena, such as extracellular signaling, as well as numerous biotechnology systems. Here, we studied the surface diffusion of individual proteins confined between two symmetric lipid bilayer membranes, under a continuum of confinement heights, using single-molecule tracking and convex lens-induced confinement as well as hybrid, kinetic Monte Carlo simulations of a generalized continuous time random walk process. Surface diffusion was observed to vary non-monotonically with confinement height, exhibiting a maximum at a height of ∼750 nm, where diffusion was nearly 40% greater than that for a semi-infinite system. This demonstrated that planar confinement can, in fact, increase surface diffusion, qualitatively validating previous theoretical predictions. Simulations reproduced the experimental results and suggested that confinement enhancement of surface diffusion for symmetric systems is limited to cases where the adsorbate exhibits weak surface sticking.

Thiolate self-assembled monolayers (SAMs) are often used to modify surface properties, including catalytic activity. These SAMs can also induce reconstruction of some metallic surfaces. Here we show, through formation and subsequent removal of thiolate SAMs from Au polycrystalline electrocatalysts, that irreversible changes to the underlying metal surface can lead to significant changes in catalytic properties, irrespective of specific interactions that might occur between thiolate molecules and various reactants. Using underpotential deposition of Pb as a surface probe, we find that across a range of different thiolates, SAMs tend to increase the proportion of (111)-facets on Au, but they simultaneously increase the defect density upon these and other facets. These changes lead to delayed onset but higher maximum activity toward formic acid oxidation, which is interpreted in terms of both the density of appropriate active site ensembles and changes to the binding isotherm for site-blocking hydroxyl species. The impacts of reconstruction are further illustrated through measured shifts in selectivity for electroreduction of crotonaldehyde, with reconstructed catalysts changing the favored product from butanal to crotyl alcohol. Thus, complex surface reorganization may play a significant role in catalytic behaviors of thiol-coated SAMs as well.

In many technological applications, DNA is confined within nanoenvironments that are smaller than the size of the unconfined polymer in solution. However, the dependence of the diffusion coefficient on molecular weight and characteristic confinement dimension remains poorly understood in this regime. Here, convex lens-induced confinement (CLiC) was leveraged to examine how the diffusion of short DNA fragments varied as a function of slit height by using single-molecule fluorescence tracking microscopy. The diffusion coefficient followed approximate power law behavior versus confinement height, with exponents of 0.27 ± 0.01, 0.32 ± 0.02, and 0.42 ± 0.06 for 692, 1343, and 2686 base pair chains, respectively. The weak dependence on slit height suggests that shorter semiflexible chains may adopt increasingly rodlike conformations and therefore experience weaker excluded-volume interactions as the confinement dimension is reduced. The diffusion coefficient versus molecular weight also exhibited apparent power law behavior, with exponents that varied slightly (from -0.89 to -0.85) with slit height, consistent with hydrodynamic interactions intermediate between Rouse and Zimm model predictions.

A long-standing goal in the field of biotechnology is to develop and understand design rules for the stabilization of enzymes upon immobilization to materials. While immobilization has sometimes been successful as a strategy to stabilize enzymes, the design of synthetic materials that stabilize enzymes remains largely empirical. We sought to overcome this challenge by investigating the mechanistic basis for the stabilization of immobilized lipases on random copolymer brush surfaces comprised of poly(ethylene glycol) methacrylate (PEGMA) and sulfobetaine methacrylate (SBMA), which represent novel heterogeneous supports for immobilized enzymes. Using several related but structurally diverse lipases, including Bacillus subtilis lipase A (LipA), Rhizomucor miehei lipase, Candida rugosa lipase, and Candida antarctica lipase B (CALB), we showed that the stability of each lipase at elevated temperatures was strongly dependent on the fraction of PEGMA in the brush layer. This dependence was explained by developing and applying a new algorithm to quantify protein surface hydrophobicity, which involved using unsupervised cluster analysis to identify clusters of hydrophobic atoms. Characterization of the lipases showed that the optimal brush composition correlated with the free energy of solvation per enzyme surface area, which ranged from -17.1 kJ/mol·nm2 for LipA to -11.8 kJ/mol·nm2 for CALB. Additionally, using this algorithm, we found that hydrophobic patches consisting of aliphatic residues had a higher free energy than patches consisting of aromatic residues. By providing the basis for rationally tuning the interface between enzymes and materials, this understanding will transform the use of materials to reliably ruggedize enzymes under extreme conditions.

While single-molecule (SM) methods have provided new insights to various catalytic processes, bimolecular reactions have been particularly challenging to study. Here, the fluorogenic Knoevenagel condensation of an aromatic aldehyde with methyl cyanoacetate promoted by surface-immobilized piperazine is quantitatively characterized using super-resolution fluorescence imaging and stochastic analysis using hidden Markov modeling (HMM). Notably, the SM results suggest that the reaction follows the iminium intermediate pathway before the formation of a fluorescent product with intramolecular charge-transfer character. Moreover, the overall process is limited by the turnover rate of the catalyst, which is involved in multiple steps along the reaction coordinate.

While many approaches to reduce fibrillation of amyloid-β (Aβ) have been aimed at slowing fibril formation, the degradation of fibrils remains challenging. We provide insight into fibril degradation as well as the inhibition of fiber formation by lipid vesicles composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine and 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol). In the presence of vesicles with the optimal lipid composition, fibril formation was inhibited up to 76%. Additionally, by tuning the lipid composition, mature fibril content decreased up to 74% and the β-sheet content of Aβ was significantly reduced. The reduction in fibril and β-sheet content was consistent with a decrease in fibril diameter and could be attributed to the chaperone-like activity of the mixed vesicles. While demonstrating this remarkable activity, our findings present new evidence that lipid composition has a significant effect on the strength of the interaction between lipid bilayers and Aβ peptides/fibrils. This understanding has intriguing therapeutic implications in treating protein misfolding diseases.

In theoretical work beginning in the 1990s, O’Shaughnessy and co-workers predicted that for lateral diffusion at a solid-liquid interface, a key step involves desorption, excursion through the liqu...

The surface diffusion of poly-l-lysine (PLL) in a planar nanoslit was studied using convex lens-induced confinement (CLiC) single-molecule tracking microscopy. Three surface chemistries were employ...

The successful incorporation of enzymes into materials through multipoint covalent immobilization (MPCI) has served as the foundation for numerous advances in diverse fields, including biocatalysis, biosensing, and chemical weapons defense. Despite this success, a mechanistic understanding of the impact of this approach on enzyme stability has remained elusive, which is critical for realizing the full potential of MPCI. Here, we showed that the stabilization of lipase upon MPCI to polymer brush surfaces resulted from the rigidification of the enzyme with an increase in the number of enzyme-brush attachments. This was evident by a 10-fold decrease in the rates of enzyme unfolding and refolding as well as a reduction of the intrinsic fluctuations of the folded and unfolded states, which was measured by single-molecule (SM) Förster Resonance Energy Transfer imaging. Moreover, our results illuminate an important trade-off between stability and activity as a function of this decrease in structural dynamics of the immobilized lipase. Notably, as the thermal stability of lipase increased, as indicated by the temperature optimum for activity of the enzyme, the specific activity of lipase decreased. This decrease in activity was attributed to a reduction in the essential motions of the folded state that are required for catalytic turnover of substrate. These results provide direct evidence of this effect, which has long been a matter of speculation. Furthermore, our findings suggest that the retention of activity and stabilization of an enzyme may be balanced by tuning the extent of enzyme attachment.

Amphiphilic Janus particles with a catalyst selectively loaded on either the hydrophobic or hydrophilic region are promising candidates for efficient and phase-selective interfacial catalysis. Here, we report the synthesis and characterization of Janus silica particles with a hydrophilic silica domain and a silane-modified hydrophobic domain produced via a wax masking technique. Palladium nanoparticles were regioselectively deposited on the hydrophobic side, and the phase selectivity of the catalytic Janus particles was established through the kinetic studies of benzyl alcohol hydrodeoxygenation (HDO). These studies indicated that the hydrophobic moiety provided nearly 100× the catalytic activity as the hydrophilic side for benzyl alcohol HDO. The reactivity was linked to the anisotropic catalyst design through microscopy of the particles. The catalysts were also used to achieve phase-specific compartmentalized hydrogenation and selective in situ catalytic degradation of a model oily pollutant in a complex oil/water mixture.

We show that protein unfolding on biomaterials may be dramatically reduced via tuning the chemical heterogeneity of the protein-material interface. Specifically, using dynamic single-molecule methods, we confirmed that the transient structure and dynamics of fibronectin (FN) may be mediated through varying the composition of random copolymer brushes. The brushes, which themselves represent an intriguing biomaterial, were composed of oligoethylene glycol and sulfobetaine methacrylate and presumably stabilized FN through partitioning and/or segregation of the copolymers. We further showed that, by controlling the transient structure and dynamics of FN, the secretion of TNF-α and IL-6 by RAW 264.7 was markedly diminished.

While both cis and trans (adhesive)-interactions cooperate in the assembly of intercellular adhesions, computational simulations have predicted that two-dimensional confinement may promote cis-oligomerization, in the absence of trans-interactions. Here, single-molecule tracking of cadherin extracellular domains on supported lipid bilayers revealed the density-dependent formation of oligomers and cis-clusters in the absence of trans-interactions. Lateral oligomers were virtually eliminated by mutating a putative cis (lateral) binding interface. At low cadherin surface coverage, wild-type and mutant cadherin diffused rapidly, consistent with the motion of a lipid molecule within a cadherin-free supported bilayer and with cadherins diffusing as monomers. Although the diffusion of mutant cadherin did not change appreciably with increasing surface coverage, the average short-time diffusion coefficient of wild-type cadherin slowed significantly above a fractional surface coverage of ∼0.01 (∼1100 molecules/μm2)....

Despite their widespread use in biocatalysis, the marginal stability of lipases can significantly limit their catalytic performance in industrial biotransformations. Here, we demonstrate that this ...

Polyelectrolyte multilayers (PEMs) have significant potential in many technologies, yet the dynamics of the constituent polymer chains remains poorly understood. We used total internal reflection fluorescence microscopy to observe microscopic single-molecule transport of fluorescently labeled poly-l-lysine (PLL) diffusing within the bulk of a PEM composed of PLL and poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) when exposed to NaCl solutions ranging in concentration from 0 to 2 M. Statistical analysis of PLL trajectories revealed motion that was nonergodic, subdiffusive, and temporally anticorrelated under all conditions. In contrast with previous macroscopic measurements of polymer diffusion within PEMs, the microscopic diffusion was 2-3 orders of magnitude faster and varied nonmonotonically with salt concentration in a way that was similar to trends previously associated with PEM swelling and viscoelastic properties. This trend in the anomalous diffusion was attributed to complex salt-dependent changes in the viscoelastic properties of the film that balanced intermolecular binding and molecular conformation.

A photocleavable membrane component was introduced into synthetic liposomes to achieve light-triggered pinocytosis-like behavior as a potential solution to the feeding requirement in protocell and bottom-up artificial cell systems. Light-triggered pinocytosis was observed in both elongated liposomes, prepared by lipid film hydration, and osmotically stressed spherical vesicles prepared by the pull-down method. Liposomes formed via lipid film hydration consistently underwent pinocytosis in cases of lobed structures or in prolate ellipsoidal structures with aspect ratios ≥2, suggesting that a critical volume-to-surface-area ratio is necessary to drive pinocytosis. When liposomes formed by the pull-down method were osmotically deformed prior to irradiation, an average of 44% exhibited pinocytosis. This light-driven pinocytosis behavior is hypothesized to be due to an asymmetric distribution of photocleavable lipid between the inner and outer leaflet, consistent with the observation that liposomes assembled a...

Surface nanostructures are increasingly more employed for controlled protein assembly on functional nanodevices, in nanobiotechnology, and in nanobiomaterials. However, the mechanism and dynamics of how nanostructures induce order in the adsorbed protein assemblies are still enigmatic. Here, we use single-molecule mapping by accumulated probe trajectories and complementary atomic force microscopy to shed light on the dynamic of in situ assembly of human plasma fibrinogen (HPF) adsorbed on nanostructured polybutene-1 (PB-1) and nanostructured polyethylene (PE) surfaces. We found a distinct lateral heterogeneity of HPF-polymer nanostructure interface (surface occupancy, residence time, and diffusion coefficient) that allow identifying the interplay between protein topographical nanoconfinement, protein diffusion mechanism, and ordered protein self-assembly. The protein diffusion analysis revealed high-diffusion polarization without correlation to the anisotropic friction characteristic of the polymer surfaces. This suggests that HPF molecules confined on the nanosized PB-1 needle crystals and PE shish-kebab crystals, respectively, undergo partial detachment and diffuse via a Sansetsukon-like nanocrawling mechanism. This mechanism is based on the intrinsic flexibility of HPF in the coiled-coil regions. We conclude that nanostructured surfaces that encourage this characteristic surface mobility are more likely to lead to the formation of ordered protein assemblies and may be useful for advanced nanobiomaterials.

Pickering emulsions stabilized by solid catalysts have received an increasing amount of attention as a reaction platform because of potential applications in the chemical industry. Here, we report a surface modification strategy for controlling the catalytic performance of Pd/Al2O3 during vanillin hydrodeoxygenation (HDO) in a water/decalin emulsion environment. A series of organophosphonic acids (PAs) were applied as modifiers to control the surface hydrophobicity, thereby determining the continuous and dispersed emulsion phases. The PAs also introduced Bronsted acid sites that promoted vanillin HDO. Reaction studies showed that the yield of the HDO product p-creosol was improved from 20% to as high as 90% upon PA modification after a reaction duration of 1 h at 50 °C. This improvement greatly depended on the surface hydrophobicity, which influenced the selectivity to different reaction pathways as well as the emulsion structures. Statistical analysis of the kinetic data confirmed the hydrophobic/hydroph...

Accumulated single-molecule observations of a fluorescent solvatochromic probe molecule were found to provide detailed local information about nanoscale hydrophobicity in polymer brushes. Using this approach, we showed that local hydrophobicity in poly(ethylene glycol) (PEG) brushes was spatially heterogeneous and increased with the surface grafting density of the polymer chains. These findings may provide an explanation for prior observations of the denaturation of surface-adsorbed proteins on PEG brushes with high grafting densities, which is believed to influence protein-mediated cell-surface interactions. Moreover, by employing the broad range of existing environmentally sensitive fluorophores, this approach may potentially be used to characterize nanoscale changes in a variety of physicochemical properties within polymeric materials.

Cooperative catalysts containing a combination of noble metal hydrogenation sites and Bronsted acid sites are critical for many reactions, including the deoxygenation (DO) of biomass-derived oxygenates in the upgrading of pyrolysis oil. One route toward the design of cooperative catalysts is to tether two different catalytically active functions so that they are in close proximity while avoiding undesirable interactions that can block active sites. Here, we deposited carboxylic acid (CA)-functionalized organophosphonate monolayers onto Al2O3-supported Pd nanoparticle catalysts to prepare bifunctional catalysts containing both Bronsted acid and metal sites. Modification with phosphonic acids (PAs) improved activity and selectivity for gas-phase DO reactions, but the degree of improvement was highly sensitive to both the presence and positioning of the CA group, suggesting a significant contribution from both the PA and CA sites. Short spacer lengths of 1–2 methylene groups between the phosphonate head and ...

Single-molecule tracking was used to characterize the mobility of poly(ethylene glycol) chains at a solid–liquid interface over a wide range of surface coverage. Trajectories exhibited intermittent motion consistent with a generalized continuous time random walk (CTRW) model, where strongly confined “waiting times” alternated with rapid flights. The presence of three characteristic regimes emerged as a function of surface coverage, based on an analysis of effective short-time diffusion coefficients, mean-squared displacement, and CTRW distributions. The dilute “site-blocking” regime exhibited increasing short-time diffusion, less confined behavior, and shorter waiting times with higher surface coverage, as anomalously strong adsorption sites were increasingly passivated. At intermediate values of surface coverage, the “crowding” regime was distinguished by the exact opposite trends (slower, more confined mobility), presumably due to increasing intermolecular interactions. The trends reversed yet again in ...

As particles flow through porous media, they follow complex pathways and experience heterogeneous environments that are challenging to characterize. Tortuosity is often used as a parameter to characterize the complexity of pathways in porous materials and is useful in understanding hindered mass transport in industrial filtration and mass separation processes. However, conventional calculations of tortuosity provide only average values under static conditions; they are insensitive to the intrinsic heterogeneity of porous media and do not account for potential effects of operating conditions. Here, we employ a high-throughput nanoparticle tracking method which enables the observation of actual particle trajectories in polymer membranes under relevant operating conditions. Our results indicate that tortuosity is not simply a structural material property but is instead a functional property that depends on flow rate and particle size. We also resolved the spatiotemporal heterogeneity of flowing particles in these porous media. The distributions of tortuosity and of local residence/retention times were surprisingly broad, exhibiting heavy tails representing a population of highly tortuous trajectories and local regions with anomalously long residence times. Interestingly, local tortuosity and residence times were directly correlated, suggesting the presence of highly confining regions that cause more meandering trajectories and longer retention times. The comprehensive information about tortuosity and spatiotemporal heterogeneity provided by these methods will advance the understanding of complex mass transport and assist rational design and synthesis of porous materials.

Reactivity of molecular catalysts can be controlled by organic ligands that regulate the steric and electronic properties of catalyst sites. This level of control has generally been unavailable for heterogeneous catalysts. We show that self-assembled monolayers (SAMs) on titania with tunable electronic properties provided fine control over surface reactivity. Controlling the identity of substituents on benzylphosphonic acid SAMs modulated the near-surface electrostatics, enabling regulation of the dehydration activity of 1-propanol and 1-butanol over a wide range, with activities and selectivities of the optimal catalyst far exceeding those of uncoated TiO2. The dipole moment of the adsorbed phosphonate was strongly correlated to the dehydration activity; kinetic measurements and computational modeling indicated that the interfacial electric field altered the transition-state structure and energy. Coating catalysts with SAMs having controllable charge distributions may provide a general approach to hetero...

Single-molecule Förster Resonance Energy Transfer (FRET) was used to study the dynamic association of mobile donor-labeled ssDNA oligonucleotides ("target") with covalently immobilized complementary acceptor-labeled ssDNA oligonucleotides ("probe"). While probe-target association events were resolved for all experiments, such FRET events were far more likely to occur in systems with complementarity and on hydrophobic, as compared to hydrophilic, surfaces. The distribution of donor-acceptor association-time intervals did not exhibit simple first-order kinetics, and when decomposed into a superposition of first-order processes, only a small fraction of events corresponded to a long-lived state that was presumed to represent true DNA hybridization, while the majority of association events were transient, representing nonspecific associations or partial hybridization. The structure of the DNA target and probe affected both the stability of the hybridized state, as well as the likelihood that an association between the two led to hybridization. In particular, the likelihood of hybridization decreased for longer target strands and for targets with stem-loop secondary structure. The presence of oligonucleotide secondary structure reduced the stability of hybridization, while greater complementarity increased stability of the hybridized state. Interestingly, increased ionic strength (i.e., greater electrostatic screening) increased the probability of hybridization but did not influence the lifetime of the hybridized state. Combined, these observations provide a nuanced view of surface-mediated DNA hybridization, where various factors independently influence the probability and stability of hybridization.

Polymer brushes, in which polymers are end-tethered densely to a grafting surface, are commonly proposed for use as stealth coatings for various biomaterials. However, although their use has received considerable attention, a mechanistic understanding of the impact of brush properties on protein adsorption and unfolding remains elusive. We investigated the effect of the grafting density of poly(ethylene glycol) (PEG) brushes on the interactions of the brush with fibronectin (FN) using high-throughput single-molecule tracking methods, which directly measure protein adsorption and unfolding within the brush. We observed that, as grafting density increased, the rate of FN adsorption decreased; however, surface-adsorbed FN unfolded more readily, and unfolded molecules were retained on the surface for longer residence times relative to those of folded molecules. These results, which are critical for the rational design of PEG brushes, suggest that there is a critical balance between protein adsorption and conformation that underlies the utility of such brushes in physiological environments.

Polymers are found near surfaces and interfaces in a wide range of chemical and biological systems, and the structure and dynamics of adsorbed polymer chains have been the subject of intense interest for decades. While polymer structure is often inferred from dynamic measurements in bulk solution, this approach has proven difficult to implement at interfaces, and the understanding of interfacial polymer conformation remains elusive. Here we used single-molecule tracking to study the interfacial diffusion of isolated poly(ethylene glycol) molecules at oil-water interfaces. Compared to diffusion in dilute aqueous solution, which exhibited the expected dependence of the diffusion coefficient (D) upon molecular weight (M) of D ∼ M(-1/2) for a Gaussian chain, the behavior at the interface was approximately D ∼ M(-2/3), suggesting a significantly more expanded polymer conformation, despite the fact that the oil was a poor solvent for the polymer. Interestingly, this scaling remained virtually unchanged over a wide range of oil viscosity, despite the fact that at low viscosities the magnitude of the diffusion coefficient was consistent with expectations based on viscous drag (i.e., Stokes-Einstein diffusion), and for high viscosity oil, the interfacial mobility was much faster than expected and consistent with the type of intermittent hopping transport observed at the solid-liquid interface. The dependence on molecular weight, in both regimes, was consistent with results from both self-consistent field theory and previous Monte Carlo simulations, suggesting that an adsorbed polymer chain adopted a partially swollen (loop-train-tail) interfacial conformation.

The surface dynamics of individual surfactant and polymer molecules on thermally responsive polymer brushes (poly(N-isopropylacrylamide), PNIPAAM) were studied using high throughput single molecule tracking microscopy. The probe molecules universally exhibited intermittent hopping motion, in which the diffusion switched between mobility and confinement with a broad distribution of waiting times; this was analyzed in the context of a continuous time random walk (CTRW) model described using “waiting time” and “flight length” distributions. We found that the surface mobility, which was affected by waiting times and flight lengths, of both probe molecules increased abruptly with temperature above the 32 °C lower critical solution temperature (LCST) transition of the PNIPAAM brush. In particular, above the LCST, where the polymer brush collapsed into a more hydrophobic dense polymer film, the effective diffusion coefficients and mobile fraction of probe molecule increased, suggesting that mobility was inhibite...

High-throughput single-molecule total internal reflection fluorescence microscopy was used to investigate the effects of pH and ionic strength on bovine serum albumin (BSA) adsorption, desorption, and interfacial diffusion at the aqueous-fused silica interface. At high pH and low ionic strength, negatively charged BSA adsorbed slowly to the negatively charged fused silica surface. At low pH and low ionic strength, where BSA was positively charged, or in solutions at higher ionic strength, adsorption was approximately 1000 times faster. Interestingly, neither surface residence times nor the interfacial diffusion coefficients of BSA were influenced by pH or ionic strength. These findings suggested that adsorption kinetics were dominated by energy barriers associated with electrostatic interactions, but once adsorbed, protein-surface interactions were dominated by short-range nonelectrostatic interactions. These results highlight the ability of single-molecule techniques to isolate elementary processes (e.g., adsorption and desorption) under steady-state conditions, which would be impossible to measure using ensemble-averaging methods.

Transport at solid-liquid interfaces is critical to self-assembly, biosensing, and heterogeneous catalysis, but surface diffusion remains difficult to characterize and rationally manipulate, due to the inherent heterogeneity of adsorption on solid surfaces. Using single-molecule tracking, we characterized the diffusion of a fluorescent long-chain surfactant on a hydrophobic surface, which involved periods of confinement alternating with bulk-mediated "flights". The concentration of methanol in solution was varied to tune the strength of the hydrophobic surface-molecule interaction. The frequency of confinement had a nonmonotonic dependence on methanol concentration that reflected the relative influence of anomalously strong adsorption sites. By carefully accounting for the effect of this surface heterogeneity, we demonstrated that flight lengths increased monotonically as the hydrophobic attraction decreased, in agreement with theoretical predictions for bulk-mediated surface diffusion. The theory provided an accurate description of surface diffusion, despite the system being heterogeneous, and can be leveraged to optimize molecular search and assembly processes.

Using high throughput single-molecule total internal reflection fluorescence microscopy (TIRFM), we have acquired molecular trajectories of bovine serum albumin (BSA) and hen egg white lysozyme during protein layer formation at the silicone oil-water interface. These trajectories were analyzed to determine the distribution of molecular diffusion coefficients, and for signatures of molecular crowding/caging, including subdiffusive motion and temporal anticorrelation of the instantaneous velocity vector. The evolution of these properties with aging time of the interface was compared with dynamic interfacial tension measurements. For both lysozyme and BSA, we observed an overall slowing of protein objects, the onset of both subdiffusive and anticorrelated motion (associated with crowding), and a decrease in the interfacial tension with aging time. For lysozyme, all of these phenomena occurred virtually simultaneously, consistent with a homogeneous model of layer formation that involves gradual crowding of weakly interacting proteins. For BSA, however, the slowing occurred first, followed by the signatures of crowding/caging, followed by a decrease in interfacial tension, consistent with a heterogeneous model of layer formation involving the formation of protein clusters. The application of microrheological methods to single molecule trajectories described here provides an unprecedented level of mechanistic interpretation of interfacial events that occurred over a wide range of interfacial protein coverage.

Using high-throughput single-molecule tracking, we studied the diffusion of poly(ethylene glycol) chains at the interface between water and a hydrophobic surface patterned with an array of hexagonally arranged nanopillars. Polymer molecules displayed anomalous diffusion; in particular, they exhibited intermittent motion (i.e., immobilization and "hopping") suggestive of continuous-time random walk (CTRW) behavior associated with desorption-mediated surface diffusion. The statistics of the molecular trajectories changed systematically on surfaces with pillars of increasing height, exhibiting motion that was increasingly subdiffusive and with longer waiting times between diffusive steps. The trajectories were well-described by kinetic Monte Carlo simulations of CTRW motion in the presence of randomly distributed permeable obstacles, where the permeability (the main undetermined parameter) was conceptually related to the obstacle height. These findings provide new insights into the mechanisms of interfacial transport in the presence of obstacles and on nanotopographically patterned surfaces.

Porous materials are used extensively in industrial filtration and mass separation processes, but it is often difficult to predict their mass transport behavior because porous materials are an inherently heterogeneous medium and multiple microscopic mechanisms can lead to macroscopic changes in transport. To provide a microscopic view of hindered porous transport, we present the results of single-particle tracking experiments in which we followed the diffusive motion of individual nanoparticles in commercial filtration media. We compared two materials, glass fiber and nitrocellulose, with similar nominal characteristics, but we found that the diffusion behavior of the embedded particles differed significantly. While diffusion in the glass fiber material was nearly unhindered, the dynamics were heterogeneous and significantly slowed in the nitrocellulose. We rationalized the observations based on differences in geometric hindrance, particle binding, and hydrodynamic interactions. Our results highlight the ...

The efficiency of chromatographic separations decreases markedly when peaks exhibit asymmetry (e.g., "peak tailing"). Theoretically, these effects can arise from heterogeneous adsorption kinetics. To investigate the nature and consequences of such heterogeneity, we used a combination of single-molecule imaging and reversed-phase liquid chromatography (RPLC). In both single-molecule and macroscopic RPLC experiments, the stationary phase was hydrophobic end-capped (trimethylsilyl-functionalized) silica, which we exposed to different methanol/water solutions (50%-62% methanol), containing a fluorescent fatty acid analyte. Super-resolution maps based on single-molecule observations revealed rare, strong adsorption sites with activity that varied significantly with methanol concentration. The adsorption and desorption kinetics on the strong sites were heterogeneous and positively correlated, suggesting a broad underlying distribution of site binding energies. Adsorption equilibrium on the strong sites was more sensitive to solution conditions than overall retention measured in RPLC experiments, suggesting that the effect of strong sites on the overall adsorption kinetics should change with solution conditions. Interestingly, in RPLC experiments, peak tailing had a nonmonotonic dependence on methanol concentration within the range studied. Using the stochastic model of chromatography, we showed quantitatively that our single-molecule kinetic results were consistent with this macroscopic trend. This approach to identifying and quantifying adsorption sites should be useful for designing better chromatographic separations and for identifying the role of heterogeneous surface chemistry in molecular dynamics.

Thiolate self-assembled monolayers (SAMs) were used to block specific active sites on Pd/Al2O3 during the hydrogenation of furfural to elucidate site requirements for each process involved in this ...

Rationally designing and producing suitable catalysts to promote specific reaction pathways remains a major objective in heterogeneous catalysis. One approach involves using traditional catalytic materials modified with self-assembled monolayers (SAMs) to create a more favorable surface environment for specific product formation. A major advantage of SAM-based modifiers is their tendency to form consistent, highly ordered assembly structures on metal surfaces. In addition, both the attachment chemistry and tail structures can easily be tuned to facilitate specific interactions between reactants and the catalyst. In this Account, we summarize our recent modification approaches for tuning monolayer structure to improve catalytic performance for hydrogenation reactions on palladium and platinum catalysts. Each approach serves to direct selectivity by tuning a particular aspect of the system including the availability of specific active sites (active-site selection), intermolecular interactions between the reactants and modifiers (molecular recognition), and general steric or crowding effects. We have demonstrated that the tail moiety can be tuned to control the density of SAM modifiers on the surface. Infrared spectra of adsorbed CO probe molecules reveal that increasing the density of the thiols restricts the availability of contiguous active sites on catalyst terraces while maintaining accessibility to sites located at particle edges and steps. This technique was utilized to direct selectivity for the hydrogenation of furfural. Results obtained from SAM coatings with different surface densities indicated that, for this reaction, formation of the desirable products occurs primarily at particle edges and steps, whereas the undesired pathway occurs on particle terrace sites. As an alternative approach, the tail structure of the SAM precursor can be tuned to promote specific intermolecular interactions between the modifier and reactant in order to position reactant molecules in a desired orientation. This technique was utilized for the hydrogenation of cinnamaldehyde, which contains an aromatic phenyl moiety. By using a phenyl-containing SAM modifier with an appropriate tether length,90% selectivity toward reaction of the aldehyde group was achieved. In contrast, employing a modifier where the phenyl moiety was closer to the catalyst surface biased selectivity toward the hydrogenation of the C═C bond due to reorienting the molecule to a more "lying down" conformation. In addition to approaches that target specific interactions between the reactant and modified catalyst, we have demonstrated the use of SAMs to impose a steric or blocking effect, for example, during the hydrogenation of polyunsaturated fatty acids. The SAMs facilitated hydrogenation of polyunsaturated to monounsaturated fatty acids but inhibited further hydrogenation to the completely saturated species due to the sterically hindered, single "kink" shape of the monounsaturated product. The recent contributions discussed in this Account demonstrate the significant potential for this approach to design improved catalysts and to develop a deeper understanding of mechanistic effects due to the near surface environment.

Ferritin has a binuclear non-heme iron active site that functions to oxidize iron as a substrate for formation of an iron mineral core. Other enzymes of this class have tightly bound diiron cofactor sites that activate O2 to react with substrate. Ferritin has an active site ligand set with 1-His/4-carboxylate/1-Gln rather than the 2-His/4-carboxylate set of the cofactor site. This ligand variation has been thought to make a major contribution to this biferrous substrate rather than cofactor site reactivity. However, the Q137E/D140H double variant of M ferritin, has a ligand set that is equivalent to most of the diiron cofactor sites, yet did not rapidly react with O2 or generate the peroxy intermediate observed in the cofactor sites. Therefore, in this study, a combined spectroscopic methodology of circular dichroism (CD)/magnetic CD (MCD)/variable temperature, variable field (VTVH) MCD has been applied to evaluate the factors required for the rapid O2 activation observed in cofactor sites. This methodology defines the coordination environment of each iron and the bridging ligation of the biferrous active sites in the double and corresponding single variants of frog M ferritin. Based on spectral changes, the D140H single variant has the new His ligand binding, and the Q137E variant has the new carboxylate forming a μ-1,3 bridge. The spectra for the Q137E/D140H double variant, which has the cofactor ligand set, however, reflects a site that is more coordinately saturated than the cofactor sites in other enzymes including ribonucleotide reductase, indicating the presence of additional water ligation. Correlation of this double variant and the cofactor sites to their O2 reactivities indicates that electrostatic and steric changes in the active site and, in particular, the hydrophobic nature of a cofactor site associated with its second sphere protein environment, make important contributions to the activation of O2 by the binuclear non-heme iron enzymes.

The dynamics of polymers adsorbed to a solid surface are important in thin-film formation, adhesion phenomena, and biosensing applications, but they are still poorly understood. Here we present tracking data that follow the dynamics of isolated poly(ethylene glycol) chains adsorbed at a hydrophobic solid-liquid interface. We found that molecules moved on the surface via a continuous-time random walk mechanism, where periods of immobilization were punctuated by desorption-mediated jumps. The dependence of the surface mobility on molecular weight (2, 5, 10, 20, and 40 kg/mol were investigated) suggested that surface-adsorbed polymers maintained effectively three-dimensional surface conformations. These results indicate that polymer surface diffusion, rather than occurring in the two dimensions of the interface, is dominated by a three-dimensional mechanism that leads to large surface displacements and significant bulk-surface coupling.

Certain salts in aqueous solution are known to significantly increase the affinity of molecules with hydrophobic moieties for a hydrophobic interface, but the mechanism of this effect is poorly understood. We used single-molecule total internal reflection fluorescence microscopy to directly observe the underlying dynamic interfacial phenomena for a fluorescent fatty acid probe molecule at a self-assembled monolayer surface. Both NaF and NaSCN increased the surface affinity of the probe from that observed in pure water, and consistent with expectations, the surface affinity was greater in the presence of NaF than that with NaSCN. Notably, the primary cause of the increase in surface affinity was specifically due to an increase in the absolute rate of adsorption from solution. In contrast, the surface residence time and the surface diffusion coefficient of the probe molecules did not depend significantly on the solution conditions.

Aptamer-ligand binding events, involving small molecule targets, at a surfactant-laden aqueous/liquid crystal (LC) interface were found to trigger a LC reorientation that can be observed in real-time using polarized light. The response was both sensitive and selective: reorientation was observed at target concentrations on the order of the aptamer dissociation constant, but no response was observed in control experiments with target analogues. Circular dichroism and resonance energy transfer experiments suggested that the LC reorientation was due to a conformational change of the aptamer upon target binding. Specifically, under conditions where aptamer-ligand binding induced a conformational change from a relaxed random coil to more intricate secondary structures (e.g., double helix, G-quadruplex), a transition from planar to homeotropic LC orientation was observed. These observations suggest the potential for a label-free LC-based detection system that can simultaneously respond to the presence of both small molecules and nucleic acids.

Self-assembled monolayers (SAMs) were prepared from a novel two-tailed partially fluorinated thiol (F8C11/C16), possessing one hydrocarbon chain and one chain with an extended fluorinated segment, and from mixtures of F8C11/C16 and hexadecanethiol (C16) on gold, with the expectation that the internal chemical dissimilarity and wedge-like shape of F8C11/C16 would lead to unique self-organizational motifs. The SAMs were systematically characterized using ellipsometry, atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), contact angle goniometry, and polarization modulation infrared reflection-absorption spectroscopy (PM-IRRAS). Based on this characterization, the one-component F8C11/C16 SAMs exhibited relatively poor molecular organization compared to traditional alkanethiols, forming low coverage monolayers with significant molecular disorder. However, the series of mixed SAMs formed from F8C11 and F8C11/C16 were anomalously well ordered as indicated by film thickness, surface coverage, and the frequencies of characteristic vibrational modes. AFM images of these mixed SAMs exhibited nanoscale fibrillar structures in a birds-nest morphology, suggesting that in the presence of a C16 matrix, the F8C11/C16 component organized into the two-dimensional analogue of discrete bilayers. Control experiments involving mixed SAMs comprised of F8C11/C16 and a single-tailed partially fluorinated thiol (F8C11) or C16 and F8C11 exhibited no appreciable indication of interesting self-organization beyond an evenly dispersed mixing of the thiolates or phase separation, respectively.

Single-molecule total internal reflection fluorescence microscopy was used to observe the dynamic behavior of polycytosine single-stranded DNA (ssDNA) (1-50 nucleotides long) at the interface between aqueous solution and hydrophilic (oligoethylene glycol-modified fused silica, OEG) and hydrophobic (octadecyltriethoxysilane-modified fused silica, OTES) solid surfaces. High throughput molecular tracking was used to determine >75,000 molecular trajectories for each molecular length, which were then used to calculate surface residence time and squared displacement (i.e., "step-size") distributions. On hydrophilic OEG surfaces, the surface residence time increased systematically with ssDNA chain length, as expected due to increasing molecule-surface interactions. Interestingly, the residence time decreased with increasing ssDNA length on the hydrophobic OTES surface, particularly for longer chains. Similarly, the interfacial mobility of polynucleotides slowed with increasing chain length on OEG, but became faster on OTES. On OTES surfaces, the rates associated with desorption and surface diffusion exhibited the distinctive anomalous temperature dependence that is characteristic of hydrophobic interactions for short-chain species but not for longer chains. These combined observations suggest that long oligonucleotides adopt conformations minimizing hydrophobic interactions, e.g., by internal sequestration of hydrophobic nucleobases.

Custom-designed surfactants, known as "linactants", have the ability to reduce the line tension between coexisting phases within mixed monolayers of chemically dissimilar compounds at the air-water interface. Thus far, linactants have been successfully identified for only one type of chemical dissimilarity, involving mixed monolayers of hydrocarbon and fluorocarbon surfactants. In the present work, we have pursued a more general interpretation of linactant compounds by extending the concept to a new system that is comprised of a mixture of aliphatic (pentadecanoic acid) and aromatic (p-terphenyl carboxylic acid) compounds. We found that the "bare" line tension between phases of this mixed monolayer was ~4 pN, and within the same order of magnitude as our previous measurement in mixed monolayers containing hydrocarbons and fluorocarbons. Furthermore, we examined a homologous series of potential linactant compounds possessing an aliphatic tail of variable length and a p-terphenyl block. We determined that linactants with longer tails were able to reduce the line tension more efficiently and effectively. In particular, the addition of only 0.14% of a linactant with an 11-carbon chain reduced the line tension by more than a factor of 2. We hypothesize that the efficiency of this particular linactant is associated with its long tail; this creates strong van der Waals interactions with the aliphatic chains and enables the tail to adopt conformations that facilitate π-stacking interactions with the aromatic compounds within the monolayer.

The interactions between adsorbate molecules and hydrophobic surfaces are of significant interest due to their importance in a variety of biological and separation processes. However, it is challenging to extrapolate macroscopic ensemble-averaged force measurements to molecular-level phenomena. Using total internal reflection fluorescence microscopy to image individual molecules at hydrophobic solid-aqueous interfaces, we directly observed dynamic behavior associated with the interactions between fluorescently labeled dodecanoic acid (our probe molecules) and self-assembled monolayers (SAM) comprising n-alkyltriethoxysilanes with systematically increasing chain length (from n = 4-18). In all cases, we observed at least two characteristic surface residence times and two diffusive modes, suggesting the presence of multiple distinct adsorbed populations. In general, the mean surface residence time increased and the mobility decreased with increasing SAM chain length, consistent with stronger probe-surface interactions. However, these trends were not primarily due to changes in characteristic residence times or diffusion coefficients associated with the individual populations but rather to a dramatic increase in the fraction associated with the long-lived slow-moving population(s) on long-chain SAMs. In particular, on longer (16-18 carbon) alkylsilane monolayers, the probe molecule exhibited far fewer desorption-mediated "flights" than on short (4-6 carbon) monolayers. Additionally, probes on the longer chain surfaces were much more likely to exhibit extended surface residence times as opposed to short transient surface visits.

Large-scale quantum and molecular mechanical methods (QM/MM) and QM calculations were carried out on the soluble Δ(9) desaturase (Δ(9)D) to investigate various structural models of the spectroscopically defined peroxodiferric (P) intermediate. This allowed us to formulate a consistent mechanistic picture for the initial stages of the reaction mechanism of Δ(9)D, an important diferrous nonheme iron enzyme that cleaves the C-H bonds in alkane chains resulting in the highly specific insertion of double bonds. The methods (density functional theory (DFT), time-dependent DFT (TD-DFT), QM(DFT)/MM, and TD-DFT with electrostatic embedding) were benchmarked by demonstrating that the known spectroscopic effects and structural perturbation caused by substrate binding to diferrous Δ(9)D can be qualitatively reproduced. We show that structural models whose spectroscopic (absorption, circular dichroism (CD), vibrational and Mössbauer) characteristics correlate best with experimental data for the P intermediate correspond to the μ-1,2-O(2)(2-) binding mode. Coordination of Glu196 to one of the iron centers (Fe(B)) is demonstrated to be flexible, with the monodentate binding providing better agreement with spectroscopic data, and the bidentate structure being slightly favored energetically (1-10 kJ mol(-1)). Further possible structures, containing an additional proton or water molecule are also evaluated in connection with the possible activation of the P intermediate. Specifically, we suggest that protonation of the peroxide moiety, possibly preceded by water binding in the Fe(A) coordination sphere, could be responsible for the conversion of the P intermediate in Δ(9)D into a form capable of hydrogen abstraction. Finally, results are compared with recent findings on the related ribonucleotide reductase and toluene/methane monooxygenase enzymes.

A mechanistic understanding of single-stranded DNA (ssDNA) behavior in the near-surface environment is critical to advancing DNA-directed self-assembled nanomaterials. A new approach is described that uses total internal reflection fluorescence microscopy to measure resonance energy transfer at the single-molecule level, providing a mechanistic understanding of the connection between molecular conformation and interfacial dynamics near amine-modified surfaces. Large numbers (10(5)) of ssDNA trajectories were observed, permitting dynamic correlation of molecular conformation with desorption and surface mobility. On the basis of dynamic behavior, molecules could be designated as members of the more common coiled population or a rare, weakly bound conformation. Molecules in the coiled state generally exhibited slow diffusion and conformational fluctuations that decreased with increasing average end-to-end distance. Lattice simulations of adsorbed self-avoiding polymers successfully predicted these trends. In contrast, the weakly bound conformation, observed in about 5% of molecules, had a large end-to-end distance but demonstrated conformational fluctuations that were much higher than predicted by simulations for adsorbed flexible chains. This conformation correlated positively with desorption events and led to fast diffusion, indicating weak surface associations. Understanding the role of the weakly bound conformation in DNA hybridization, and how solution conditions and surface properties may favor it, could lead to improved self-assembled nanomaterials.

A Genetic Algorithm (GA) is a stochastic optimization technique based on the mechanisms of biological evolution. These algorithms have been successfully applied in many fields to solve a variety of complex nonlinear problems. While they have been used with some success in chemical problems such as fitting spectroscopic and kinetic data, many have avoided their use due to the unconstrained nature of the fitting process. In engineering, this problem is now being addressed through incorporation of adaptive penalty functions, but their transfer to other fields has been slow. This study updates the Nanakorrn Adaptive Penalty function theory, expanding its validity beyond maximization problems to minimization as well. The expanded theory, using a hybrid genetic algorithm with an adaptive penalty function, was applied to analyze variable temperature variable field magnetic circular dichroism (VTVH MCD) spectroscopic data collected on exchange coupled Fe(II)Fe(II) enzyme active sites. The data obtained are described by a complex nonlinear multimodal solution space with at least 6 to 13 interdependent variables and are costly to search efficiently. The use of the hybrid GA is shown to improve the probability of detecting the global optimum. It also provides large gains in computational and user efficiency. This method allows a full search of a multimodal solution space, greatly improving the quality and confidence in the final solution obtained, and can be applied to other complex systems such as fitting of other spectroscopic or kinetics data.