Spectroscopic characterization of rare events in colloidal particle stochastic thermodynamics.

Given the remarkable developments in synthetic control over chemical and physical properties of colloidal particles, it is interesting to see how stochastic thermodynamics studies may be performed with new, surrogate, or hybrid model systems. In the present work, we apply stochastic dynamics and nonlinear optical light-matter interaction simulations to study nonequilibrium trajectories of individual Yb (III):Er (III) colloidal particles driven by two-dimensional dynamic optical traps. In addition, we characterize the role of fluctuations at the single-particle level by analyzing position trajectories and time-dependent upconversion emission intensities. By integrating these two complementary perspectives, we show how the methods developed here can be used to characterize rare events.

Rich stochastic dynamics of co-doped Er:Yb fluorescence upconversion nanoparticles in the presence of thermal, non-conservative, harmonic and optical forces.

The stochastic dynamics of individual co-doped Er:Yb upconversion nanoparticles (UCNP) were investigated from experiments and simulations. The UCNP were characterized by high-resolution scanning electron microscopy, dynamic light scattering, and zeta potential measurements. Single UCNP measurements were performed by fluorescence upconversion micro-spectroscopy and optical trapping. The mean-square displacement (MSD) from single UCNP exhibited a time-dependent diffusion coefficient which was compared with Brownian dynamics simulations of a viscoelastic model of harmonically bound spheres. Experimental time-dependent two-dimensional trajectories of individual UCNP revealed correlated two-dimensional nanoparticle motion. The measurements were compared with stochastic trajectories calculated in the presence of a non-conservative rotational force field. Overall, the complex interplay of UCNP adhesion, thermal fluctuations and optical forces led to a rich stochastic behavior of these nanoparticles.

Characterizing Slow Photochemical Reaction Kinetics by Enhanced Sampling of Rare Events with Capillary Optical Fibers and Kramers' Theory.

Characterization of slow chemical reactions is essential for assessing catalytic efficiency in chemistry and biology. Traditionally, chemical reaction rates are obtained from population relaxation kinetics measurements and the Arrhenius equation. Unfortunately, it is difficult to use this approach to characterize reactions wherein concentrations change slowly. Thus, it is interesting to see whether a dynamical view of chemical reactions may be used to obtain the reaction rates of slow processes. In the present work, we perform Brownian dynamics simulations of an asymmetric double-well potential to investigate how enhanced sampling of barrier crossing at transition states improves the characterization of reaction rate constants. We then present the design of a liquid-filled capillary optical fiber-based fluorescence spectrometer, which, like rare events, is also based on Poissonian statistics. We use the instrument to characterize the slow photochemical degradation kinetics of poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] (MEH-PPV) in o-dichlorobenzene. We have employed in situ optical microscopy measurements and electrodynamics simulations to characterize the excitation beam profile inside a liquid-filled capillary fiber. We compare the cuvette and capillary fiber sample holders and show that the MEH-PPV fluorescence line shape is independent of the sample holder, as expected. We characterize the photochemical degradation kinetics of MEH-PPV in o-dichlorobenzene solutions placed in the cuvette versus that in the capillary fiber. We observe small and slow changes in the time-dependent fluorescence spectra when the degradation reaction is performed in the cuvette. On the other hand, we are able to characterize reactant-concentration decay and product-concentration buildup from the time-dependent fluorescence spectra recorded during photochemical degradation of MEH-PPV performed inside the capillary optical fiber. Ultrafast optically heterodyne-detected optical Kerr effect spectroscopy and multimode Brownian oscillator analysis provide further insights into the role of bath oscillator modes of friction in the mechanism of MEH-PPV photochemical degradation. Overall, the work presented herein shows that slow photochemical degradation kinetics of MEH-PPV can be successfully and efficiently assessed in the capillary fiber fluorescence spectrometer.

Effective targeting of proton transfer at ground and excited states of ortho-(2'-imidazolyl)naphthol constitutional isomers.

Steady-state and time-resolved spectroscopy and quantum chemical computational studies were employed to investigate ground and excited state proton transfer of a novel series of ortho-(1H-imidazol-2-yl)naphthol constitutional isomers: 1-(1H-imidazol-2-yl)naphthalen-2-ol (1NI2OH), 2-(1H-imidazol-2-yl)naphthalen-1-ol (2NI1OH) and 3-(1H-imidazol-2-yl)naphthalen-2-ol (3NI2OH). Proper Near Attack Conformations (NACs) involving a strong intramolecular hydrogen bond between the naphthol moiety and the ortho-imidazole group account for the highest ground state acidity of 2NI1OH compared with 1NI2OH and 3NI2OH. Moreover, ESIPT for 2NI1OH and 3NI2OH is further associated with planar chelate H-ring formation whereas 1NI2OH shows the highest ESIPT barrier and a noncoplanar imidazole group. In addition to energetic and structural requirements, the final state also depends on electronic configuration of the ESIPT product with the neutral 3NI2OH showing an ICT effect that correlates with the excited state pKa of the cationic species.

Towards in situ fluorescence spectroscopy and microscopy investigations of asphaltene precipitation kinetics.

We perform a spectroscopic analysis of asphaltene in solution and in crude oil with the goal of designing an optical probe of asphaltene precipitation inside high-pressure cells. Quantitative analysis of steady-state spectroscopic data is employed to identify fluorescence and Raman contributions to the observed signals. Time-resolved fluorescence spectroscopy indicates that fluorescence lifetime can be used as a spectroscopic probe of asphaltene in crude oil. Quantitative confocal laser-scanning microscopy studies of asphaltene in n-heptane are used to calculate particle-size distributions as a function of time, both at the sample surface and asphaltene interior. The resulting precipitation kinetics is well described by stochastic numerical simulations of diffusion-limited aggregation. Based on these results, we present the design and construction of an apparatus to optically probe the in situ precipitation of asphaltene suitable for studies inside high pressure cells. Design considerations include the use of a spatial light modulator for aberration correction in microscopy measurements, together with the design of epi-fluorescence spectrometer, both fiber-based and for remote sensing fluorescence spectroscopy.

Interaction between an organic dye in water and sand packs in a flume system.

The sorption kinetics of methylene blue (MB), a standard compound in the American Society for Testing and Materials tests, on natural sand in a batch system at a reciprocal shaking speed of 120 rpm is fast, with equilibrium and surface coverage attained in minutes. When the same experiment is carried out in a recirculating flume, adsorption is much slower, with lifetimes increasing up to several months in the flume. Sorption retardation is dependent on the diffusion coefficient of the dye and on the depth of penetration of the MB layer in sand. The experimental results suggest that, in field experiments, formation of thin films dramatically inhibits the sorption kinetics and, in a closed system, such as a lake or reservoir, contaminants will remain in the water column for long periods, with very slow penetration in the sediment layer. In rivers, the contaminant will travel farther with less penetration into the sediment layer, compared to more static systems.

Controlling plasmonic wave packets in silver nanowires.

Three-dimensional finite-difference time-domain simulations were performed to explore the excitation of surface plasmon resonances in long silver (Ag) nanowires. In particular, we show that it is possible to generate plasmonic wave packets that can propagate along the nanowire by exciting superpositions of surface plasmon resonances. By using an appropriately chirped pulse, it is possible to transiently achieve localization of the excitation at the distal end of the nanowire. Such designed coherent superpositions will allow realizing spatiotemporal control of plasmonic excitations for enhancing nonlinear responses in plasmonic "circuits".

Spectral tuning in photoactive yellow protein by modulation of the shape of the excited state energy surface.

Protein-chromophore interactions in photoreceptors often shift the chromophore absorbance maximum to a biologically relevant spectral region. A fundamental question regarding such spectral tuning effects is how the electronic ground state S(0) and excited state S(1) are modified by the protein. It is widely assumed that changes in energy gap between S(0) and S(1) are the main factor in biological spectral tuning. We report a generally applicable approach to determine if a specific residue modulates the energy gap, or if it alters the equilibrium nuclear geometry or width of the energy surfaces. This approach uses the effects that changes in these three parameters have on the absorbance and fluorescence emission spectra of mutants. We apply this strategy to a set of mutants of photoactive yellow protein (PYP) containing all 20 side chains at active site residue 46. While the mutants exhibit significant variation in both the position and width of their absorbance spectra, the fluorescence emission spectra are largely unchanged. This provides strong evidence against a major role for changes in energy gap in the spectral tuning of these mutants and reveals a change in the width of the S(1) energy surface. We determined the excited state lifetime of selected mutants and the observed correlation between the fluorescence quantum yield and lifetime shows that the fluorescence spectra are representative of the energy surfaces of the mutants. These results reveal that residue 46 tunes the absorbance spectrum of PYP largely by modulating the width of the S(1) energy surface.

Plasmonic interactions and optical forces between au bipyramidal nanoparticle dimers.

Interparticle forces that can be driven by applied (optical) fields could lead to the formation of new particle arrangements when assembled in arrays. Furthermore, the potentially large interactions and large local fields associated with plasmon excitations in anisotropic nanoparticles can lead to enhanced nonlinear responses and applications for sensing. These and other applications would benefit from simulations of spectra and forces arising from plasmonic interactions. We present the results of rigorous three-dimensional, finite-difference, time-domain calculations of near- and far-field properties of pairs of Au bipyramidal nanoparticles in three different configurations: side-by-side, head-to-tail, and face-on. The absorption and scattering spectra depend strongly on the geometry as well as on the interparticle separation, as intuitively expected from a dipole coupling picture. Bipyramidal dimers in head-to-tail and face-on geometries exhibit an increasingly red-shifted (longitudinal) plasmon resonance with decreasing separation, whereas side-by-side dimers exhibit a blue shift. Large resonant field enhancements at the gap between particles in a head-to-tail configuration indicate the strong coupling of plasmonic modes. The Maxwell stress tensor formalism is employed to calculate the optical force one particle exerts on the other. Both significant attraction and weak repulsion can be obtained, depending on the relative arrangement of the particles. The force between bipyramids in the head-to-tail configuration can be greater than 10 times the force between pairs of Au nanospheres with the same volume. Experimental linear scattering spectra of particles trapped using the plasmon-resonance-based optical trapping method are found to be consistent with two particles trapped in the side-by-side configuration.

Assessing the dephasing dynamics of water from linear field-resolved pulse propagation experiments and simulations in highly absorbing solutions.

We measure and simulate electric field distortions resulting from propagation of mid-infrared pulses that are resonant with the OH stretch vibration through optically dense HDO:D(2)O. These distortions are characterized experimentally by full-field-resolved time- and frequency-domain measurements, specifically cross-correlation frequency-resolved optical gating and spectral interferometry, establishing amplitude and phase of the signal fields. Correlation-function finite-difference time-domain (CF-FDTD) simulations using response functions for the OH-stretching vibration, obtained from nonlinear spectroscopic studies reported by others, show that details of the line shape functions are manifested in the measured (linear-response) spectrograms. The degree of homogeneous or inhomogeneous broadening present in the various model correlation functions is readily apparent in the measured and simulated signals. Surprisingly, the published correlation functions are shown to range from modest inhomogeneous to homogeneous line broadening. The present experimental and simulation approach is very useful for establishing the correct form of energy gap correlation functions and dephasing dynamics of IR and optical transitions. In the case of HDO:D(2)O, correlation functions with modest inhomogeneous broadening better reflect our measured responses.

Axis-dependent anisotropy in protein unfolding from integrated nonequilibrium single-molecule experiments, analysis, and simulation.

We present a comprehensive study that integrates experimental and theoretical nonequilibrium techniques to map energy landscapes along well defined pull-axis specific coordinates to elucidate mechanisms of protein unfolding. Single-molecule force-extension experiments along two different axes of photoactive yellow protein combined with nonequilibrium statistical mechanical analysis and atomistic simulation reveal energetic and mechanistic anisotropy. Steered molecular dynamics simulations and free-energy curves constructed from the experimental results reveal that unfolding along one axis exhibits a transition-state-like feature where six hydrogen bonds break simultaneously with weak interactions observed during further unfolding. The other axis exhibits a constant (unpeaked) force profile indicative of a noncooperative transition, with enthalpic (e.g., H-bond) interactions being broken throughout the unfolding process. Striking qualitative agreement was found between the force-extension curves derived from steered molecular dynamics calculations and the equilibrium free-energy curves obtained by Jarzynski-Hummer-Szabo analysis of the nonequilibrium work data. The anisotropy persists beyond pulling distances of more than twice the initial dimensions of the folded protein, indicating a rich energy landscape to the mechanically fully unfolded state. Our findings challenge the notion that cooperative unfolding is a universal feature in protein stability.

Field-resolved measurement of reaction-induced spectral densities by polarizability response spectroscopy.

The experimental design and theoretical description of a novel five-pulse laser spectroscopy is presented with an application to a pyridinium charge transfer complex in acetonitrile and methanol. In field-resolved polarizability response spectroscopy (PORS), an electronically resonant laser pulse first excites a solvated chromophore (reactant) and off-resonant Raman spectra of the resulting nuclear motions are measured as a function of the reaction time. The present apparatus differs from our earlier design by performing the Raman probe measurement (with fixed pulse delays) in the frequency domain. In addition, the full electric fields of the signals are measured by spectral interferometry to separate nonresonant and Raman responses. Our theoretical model shows how the PORS signal arises from nuclear motions that are displaced/driven by the photoinduced reaction. The field-resolved off-resonant (of the solute's electronic transitions) probing favors detection of solvent (as opposed to solute) dynamics coupled to the reaction. The sign of the signal represents the relative strengths of polarization responses associated with the ground and photoexcited solutions. Signatures of nonresonant and PORS signal contributions to the experimental results are analyzed with numerical calculations based on a theoretical model we have developed for reaction-induced PORS. Our model identifies two mechanisms of PORS signal generation: (i) structural relaxation induced resonance; (ii) dephasing induced resonance. In the charge transfer reaction investigated, the solvent-dependent and time-evolving (solvent) polarizability spectral density (PSD) is readily obtained. The general trend of an initial broadband inertial nuclear response followed by a decrease in the linewidth of the PSD establishes that the measured PSD is inconsistent with the approximation of a linear response. Furthermore, the explicit time evolution of the PSD is important for properly describing solvent control of reactions that do not satisfy the time-scale separability inherent to nonadiabatic kinetic models.

Field-resolved coherent Raman spectroscopy of high frequency vibrational resonances.

Electric fields of coherent Raman signals are resolved with sensitivity for high-frequency vibrational resonances utilizing a four-pulse, trapezoidal beam geometry in a diffractive optic-based interferometer. Our experiments show that the heterodyne detected signal phase is stabilized for particular terms in the third-order response function by the cancellation of inter-pulse phases. The C-H stretching modes of cyclohexane and benzene are studied under two polarization conditions. The temporal profiles of signal fields for cyclohexane exhibit a low-frequency recurrence due to the interference between the signals associated with the symmetric and asymmetric C-H stretching modes. In contrast, the electronically nonresonant polarizability response of benzene gives rise to a significant broadband signal component in addition to that associated with its C-H vibrational resonance. Time-frequency shapes of the Raman signal fields are strongly dependent on the properties of the liquid and the polarizations of the laser pulses.

Single-molecule detection of structural changes during Per-Arnt-Sim (PAS) domain activation.

The Per-Arnt-Sim (PAS) domain is a ubiquitous protein module with a common three-dimensional fold involved in a wide range of regulatory and sensory functions in all domains of life. The activation of these functions is thought to involve partial unfolding of N- or C-terminal helices attached to the PAS domain. Here we use atomic force microscopy to probe receptor activation in single molecules of photoactive yellow protein (PYP), a prototype of the PAS domain family. Mechanical unfolding of Cys-linked PYP multimers in the presence and absence of illumination reveals that, in contrast to previous studies, the PAS domain itself is extended by approximately 3 nm (at the 10-pN detection limit of the measurement) and destabilized by approximately 30% in the light-activated state of PYP. Comparative measurements and steered molecular dynamics simulations of two double-Cys PYP mutants that probe different regions of the PAS domain quantify the anisotropy in stability and changes in local structure, thereby demonstrating the partial unfolding of their PAS domain upon activation. These results establish a generally applicable single-molecule approach for mapping functional conformational changes to selected regions of a protein. In addition, the results have profound implications for the molecular mechanism of PAS domain activation and indicate that stimulus-induced partial protein unfolding can be used as a signaling mechanism.

Resolving the emission times of solute and solvent four-wave mixing signals by spectral interferometry.

Electric field-resolved transient grating measurements are used to distinguish the four-wave mixing signal emission from a resonant solute and a non-resonant solvent. The two components of the solution (i.e., solute and solvent) emit signal fields at different times with respect to the arrival of the probe pulse to the sample. This gives rise to a recurrence in the temporal profile of the total signal field. We show that the origin of this interference is the difference in relaxation time scales of the holographic gratings associated with the solute and solvent. The grating of the resonant solute relaxes on the time scale of a few picoseconds due to depopulation of its excited electronic state, whereas the electronic polarizability response of the solvent relaxes on the femtosecond time scale. This separability of responses is a general phenomenon that is particularly useful for studying weakly absorbing solute dynamics in polarizable solvents.

Optical coherence and theoretical study of the excitation dynamics of a highly symmetric cyclophane-linked oligophenylenevinylene dimer.

Optoelectronic properties of a polyphenylenevinylene-based oligomer and its paracylophane-linked dimer are studied using a variety of experimental and theoretical techniques. Despite the symmetrical structure and redshifted absorption of the dimer versus the monomer, an exciton picture is not the most appropriate. Electronic structure calculations establish changes in charge density upon optical excitation and show localized excitations that cannot be accounted for by a simple Frenkel exciton model. Visible frequency pump-probe anisotropy measurements suggest that the dimer should be considered as a three-level system with a fast, approximately 130 fs, internal conversion from the higher to lower energy excited electronic state. Signatures of nuclear relaxation processes are compared for electric field-resolved transient grating and two-dimensional photon echo spectra. These measurements reveal that nuclear relaxation occurs on similar time scales for the monomer and dimer. The connection between the spectral phase of four-wave mixing signals and the time dependent width of a nuclear wave packet is discussed. Semiempirical electronic structure and metropolis Monte Carlo calculations show that the dominant line broadening mechanisms for the monomer and dimer are associated with inter-ring torsional coordinates. Together, the theoretical calculations and electric field-resolved four-wave mixing experiments suggest that while the structure of dimer is more rigid than that of monomer, the difference in their rigidities is not sufficient to slow down excited state relaxation of dimer with respect to the monomer.

Distribution of hexavalent Cr species across the clay mineral surface-water interface.

The adsorption isotherms of Cr(VI) on kaolinite, montmorillonite, and alumina were adequately treated with Langmuir model showing behavior characteristic of single-layer adsorption. The efficiency of the adsorbents in removing Cr(VI) from water follows the order alumina > kaolinite > montmorillonite > silica. Speciation studies indicate that hydrogen chromate ions were the major adsorbed species and simultaneous adsorption of dichromate ion occurred at concentrations greater than approximately 10(-3) mol L(-1). It is most probable that the mechanism of adsorption of the hydrogen chromate ion at the surface of alumina is predominantly electrostatic adsorption, with outer sphere complex formation.