Fractional Brownian dynamics in proteins

Correlation functions describing relaxation processes in proteins and other complex molecular systems are known to exhibit a nonexponential decay. The simulation study presented here shows that fractional Brownian dynamics is a good model for the internal dynamics of a lysozyme molecule in solution. We show that both the dynamic structure factor and the associated memory function fit well the corresponding analytical functions calculated from the model. The numerical analysis is based on autoregressive modeling of time series.     

Sub-picosecond time-resolved IR spectroscopy of the vibrational dynamics of Rh (CO)2 (acac)

Sub-picosecond pulses are used to measure the transient IR spectra of vibrationally excited Rh(CO)₂ (acac) in dilute solutions of n-hexane and CCl₃H. Ground-state bleach and excited-state absorption features are observed at t_D>0, while interference-like spectra characteristic of the perturbed free induction decay (FID) of the probe polarization are seen at t_D<). At t_D>), the bleach signal exhibits an initial decay (n-hexane, 3–6 ps; CCl₃H, 2.2–4 ps) attributed to rapid v-v coupling between the symmetric and asymmetric stretch modes of the dicarbonyl, followed by much slower (n-hexane, 61 ps; CCl₃H, 101 ps) population relaxation. Calculated transient spectra and bleach decay curves obtained from a 5-level density matrix model of the coupled CO oscillators account for the data, including the effects due to perturbed FID and rapid v-v coupling.     

Collisional deactivation of highly vibrationally excited hexafluorobenzene molecules

The collisional deactivation of the internal energy of vibrationally highly excited hexafluorobenzene (HFB) molecules was examined by the analysis of ultraviolet absorption spectra of excited HFB molecules produced by excitation with an ArF(193 nm) laser. The decay time profile of the internal energy was calculated from the observed absorption decay profile of the hot molecule using the conversion relation between the absorbance by hot molecules and the internal energy. Thus the average energy 〈ΔE〉 transferred per collision was estimated by two different models; energy-independent and energy-dependent function for the decay of the internal energy. The obtained values of 〈ΔE〉 indicate that the energy-dependent model may give reasonable values for 〈ΔE〉, but as far as the value of 〈ΔE〉 is concerned, the energy-independent model is likely to be applicable to the analysis in this reaction system. The collisional deactivation mechanism of the hot HFB molecule and the heating-up effect observed at shorter wavelengths are discussed on the basis of the conversion curve.     

Instantaneous vibrational frequencies of diffusing and desorbing adsorbates: CO/Pt(111)

Electronic excitation of metal by intense laser pulses stimulates nuclear motions of adsorbates through nonadiabatic coupling, resulting in diffusion and desorption of adsorbates. These processes take place via precursor states: adsorbates whose vibrational modes with respect to substrate are highly excited. This paper reports the dynamics of precursor states of CO on Pt(111) probed by use of infrared-visible sum frequency generation with phase-sensitive detection, which allows us to obtain the second-order nonlinear susceptibility and thus the vibrational response function. Without pump pulses at 400 nm, the inverse Fourier transformation of the vibrational response function reveals a free induction decay of vibrational polarization of C-O stretching created by a short infrared pulse. The free induction decay is perturbed when an intense 400-nm pump pulse following the infrared pulse is irradiated, because diffusion and desorption of CO are induced by the pump pulse. The time evolution of instantaneous C-O stretching frequency retrieved from the perturbed free induction decay shows a redshift followed by a rapid reverse shift when the fluence of pump pulse is high enough to desorb CO. This indicates that the frustrated modes of CO is first substantially excited and then the parallel momentum of CO is converted to the normal one through mutual collisions, leading to substantial excitation of the external stretching mode of CO.     

A COMPARISON OF DECAY KINETICS OF PHOTO-PRODUCED ABSORBANCE,EPR, AND LUMINESCENCE CHANGES IN CHROMATOPHORES OF RHODOSPIRRILLUM RUBRUM*

–Quantitative comparison of the decay rate for absorbance photochanges in chromatophores of R. rubrum at the major wavelengths of peaks and troughs (280, 365, 385, 433, 605, 763, 790, 810, 850, 865, 890 nm) reveal no major differences under a variety of sample conditions. In addition, the decay kinetics of EPR phtochange at the two environmental potentials used in this study are identical with the absorbance ph;otochange decay. Decay curves for fresh chromatophores, aged chromatophores, and fresh chromatophores at high ionic strength display a variety of half times and curve shapes. All of these data however, may be fit (within 10 per cent) by the equation x=αe^8.2t+βe^0.18t by merely varying the values of α and β. This is interpreted as meaning that any single trapping site may exist in one of two major forms each of which decays following a first order or pseudo-first order reaction. Although the change in decay pattern upon aging is not reversible, that due to high ionic strength is. The time dependencies for two light emission phenomena have been measured as well as their response to the oxidation state of molecules at the trapping site. A major component of long-lived luminescence follows pseudo-second order kinetics with a half time of 38 msec. A very long lived luminescence shows an increse with time which is nearly proportional to the decay of absorbance photochanges.     

Field-induced alignment of the nematic director: studies of nuclear magnetic resonance spectral oscillations in the limit of fast director rotation

Time-resolved NMR spectroscopy is a powerful method to investigate field-induced rotation of the director in a nematic liquid crystal. The method requires that the director does not rotate significantly during the acquisition of the free induction decay and hence the NMR spectrum. We have extended the method to systems where this is not the case and the observed NMR spectra are now found to contain novel oscillatory features. To understand these oscillations, we have developed a model combining both director and spin dynamics. In addition to increasing the information content of the time-resolved NMR spectra, it also proves possible to determine the field-induced relaxation time from a single spectrum.     

Evaluation of the complexity of charge recombination kinetics in photosynthetic bacteria

Abstract Improvements in instrumentation and methodology have allowed us to collect data of high signal to noise and reliability on the kinetics of recovery of both light-induced absorbance changes and ESR signals at 95 K. The results obtained by the two methods are identical and can not be fit with a single exponential curve. The decay kinetics can be fit well with three exponential components which represent 85, 9 and 6% of the total change with rate constants of 29 s⁻¹, 69 s⁻¹ and 2.3 s⁻¹, respectively. An interesting effect by molecular oxygen on the relaxation time of the donor cation radical was found by ESR measurements at low temperatures and higher microwave power. This interaction with oxygen could be blocked by addition of small amounts (e.g. 0.05%) of organic solvents such as ethanol. A variety of systems were examined including R. rubrum whole cells and chromatophores prepared from R. rubrum and Rps. sphaeroides. R. rubrum chromatophore samples were examined at high and low light intensities, at pH values from 6 to 10, in the presence and absence of air and after equilibration in D₂O media. In all cases, the same decay kinetics were observed. It seems possible that the observed complex decay may be a characteristic of phototraps of all photosynthetic material and reflect fundamental structural and functional features yet to be uncovered.     

Quantitative analysis of backbone dynamics in a crystalline protein from nitrogen-15 spin-lattice relaxation

A detailed analysis of nitrogen-15 longitudinal relaxation times in microcrystalline proteins is presented. A theoretical model to quantitatively interpret relaxation times is developed in terms of motional amplitude and characteristic time scale. Different averaging schemes are examined in order to propose an analysis of relaxation curves that takes into account the specificity of MAS experiments. In particular, it is shown that magic angle spinning averages the relaxation rate experienced by a single spin over one rotor period, resulting in individual relaxation curves that are dependent on the orientation of their corresponding carousel with respect to the rotor axis. Powder averaging thus leads to a nonexponential behavior in the observed decay curves. We extract dynamic information from experimental decay curves, using a diffusion in a cone model. We apply this study to the analysis of spin-lattice relaxation rates of the microcrystalline protein Crh at two different fields and determine differential dynamic parameters for several residues in the protein.     

Single molecules reveal the dynamics of heterogeneities in a polymer at the glass transition

The notion of heterogeneous dynamics in glasses, that is, the spatial and temporal variations of structural relaxation rates, explains many of the puzzling features of glass dynamics. The nature and the dynamics of these heterogeneities, however, have been very controversial. Single rhodamine B molecules in poly(vinyl acetate) at the glass transition reorient through sudden jumps. With a statistical search for the most likely break points in the logarithm of the ratio of the two perpendicular fluorescence polarizations, we determine the times of these angular jumps. We interpret these jumps as an indication for individual glass rearrangements in the vicinity of the probe molecule. Time-series analysis of the resulting sequence of waiting times between jumps shows that dynamic heterogeneities in the matrix exist, but are short lived. From the correlation of the logarithm of the waiting time between subsequent jumps, we determine an upper limit for the lifetime of heterogeneities in the sample. The correlation time of τ(het) = 32 s is three times shorter than the orientational correlation time of the probe molecule, τ(orient) = 90 s, in the sample at this temperature, but 13 times longer than the structural relaxation time, τ(α) = 2.5 s, estimated for this sample from dielectric experiments. We present a model for glass dynamics in which each rearrangement in one region causes a random change in the barrier height for subsequent rearrangements in a neighboring region. This model, which equates the dynamics of the heterogeneities with the dynamics of the glass itself and thus implies a factor of one between heterogeneity lifetime and structural relaxation time, successfully reproduces the statistics of the experimentally observed waiting time sequences.     

Investigating excited state dynamics of salinixanthin and xanthorhodopsin in the near-infrared

Excited state dynamics of native Xanthorhodopsin (XR), of an XR sample with a reduced prosthetic group, and of the associated Carotenoid (CAR) salinixanthin (SX) in ethanol were investigated by hyperspectral Near Infrared (NIR) probing. Global kinetic analysis shows that: (1) unlike the transient spectra recorded in the visible, fitting of the NIR data requires only two phases of exponential spectral evolution, assigned to internal conversion from S(2) → S(1) and from S(1) → S(0) of the carotene. (2) The rate of the internal conversion from S(2) → S(1) in the reduced sample is well fit with a decay time of 130 fs, significantly longer than in XR and in SX, both of which are well fit with τ ≈ 100 fs. This increased lifetime is consistent with a ～30% efficiency of ET from SX to retinal in XR. (3) S(1) of salinixanthin is verified to lie ～12,700 cm(-1) above the ground electronic surface, excluding its involvement in the retinal sensitization in XR. (4) The oscillator strength of the S(1) → S(2) transition is determined to be no more than 0.16, despite its symmetry allowedness. (5) No long lived NIR absorbance decay assignable to the carotenoid S* state was detected in any of the samples. Inconsistencies concerning previously determined S(2) lifetimes and kinetic schemes used to model these data are discussed.     

Sub-Doppler spectra of infrared hyperfine transitions of nitric oxide using a pulse modulated quantum cascade laser: rapid passage, free induction decay, and the ac Stark effect

Using a low power, rapid (nsec) pulse-modulated quantum cascade (QC) laser, collective coherent effects in the 5 μm spectrum of nitric oxide have been demonstrated by the observation of sub-Doppler hyperfine splitting and also Autler-Townes splitting of Doppler broadened lines. For nitrous oxide, experiments and model calculations have demonstrated that two main effects occur with pulse-modulated (chirped) quantum cascade lasers: free induction decay signals, and signals induced by rapid passage during the laser chirp. In the open shell molecule, NO, in which both Λ-doubling splitting and hyperfine structure occur, laser field-induced coupling between the hyperfine levels of the two Λ-doublet components can induce a large ac Stark effect. This may be observed as sub-Doppler structure, field-induced splittings, or Autler-Townes splitting of a Doppler broadened line. These represent an extension of the types of behaviour observed in the closed shell molecule nitrous oxide, using the same apparatus, when probed with an 8 μm QC laser.     

The dynamics of the intramolecular and orientational motions of pinacyanol

The influence of viscosity on the electronic relaxation of pinacyanol in alcoholic solutions has been determined by recording, with picosecond and nanosecond resolution, the fluorescence decay at various temperatures. The results are interpreted with the aid of a model of electronic relaxation implying a molecular conformational change with no internal potential barrier and with a Boltzmann equilibrium distribution of the initial configuration. Furthermore, fluorescence depolarization analysis indicates that the reorientational relaxation of the molecule takes place on a time scale much greater than that characterizing the intramolecular geometrical change.     

Surface hopping simulation of the vibrational relaxation of I2 in liquid xenon using the collective probabilities algorithm

A surface hopping simulation of the vibrational relaxation of highly excited I(2) in liquid xenon is presented. The simulation is performed by using the collective probabilities algorithm which assures the coincidence of the classical and quantum populations. The agreement between the surface hopping simulation results and the experimental measurements for the vibrational energy decay curves at different solvent densities and temperatures is shown to be good. The overlap of the decay curves when the time axis is linearly scaled is explained in terms of the perturbative theory for the rate constants. The contribution of each solvent atom to the change of the quantum populations of the solute molecule is used to analyze the mechanism of the relaxation process     

Photoproperties of isolated cis and trans stilbene molecules

A detailed account is given of the experimental approach to measuring transient spectra of dilute gases using picosecond pulses. The picosecond continuum generated by Nd:glass laser pulses is used to probe gaseous samples and spectra are recorded in a double beam arrangement. The pump and probe pulses interact with the sample over a few centimeters by means of a dielectric waveguide. Picosecond time resolved spectra, relative fluorescence quantum yield measurements, and fluorescence spectra are reported for trans-stilbene under collision free conditions. The lifetime of the optically prepared states at 265 nm and 287 nm are 15 ps and 55 ps respectively, measured by the decay of the transient absorption. The deuteration effect is less than 20%. The variation of the fluorescence yield with vibrational energy excess in the excited state of trans is fitted to these lifetime measurements to yield the variation of nonradiative decay due to twisting of trans-stilbene. Cis-stilbene is suggested to twist in less than 1 ps. Consideration of the spectral results yields new information about the isomerization of stilbene, in particular that there exists a barrier to twisting in the isolated molecule and that vibrational energy redistribution at the trans configuration is probably not complete on the time scale of our experiments. A pictorial model for discussing constant energy relaxation phenomena is introduced.     

Pulsed field gradient NMR study of phenol binding and exchange in dispersions of hollow polyelectrolyte capsules

The distribution and exchange dynamics of phenol molecules in colloidal dispersions of submicron hollow polymeric capsules is investigated by pulsed field gradient NMR (PFG-NMR). The capsules are prepared by layer-by-layer assembly of polyelectrolyte multilayers on silica particles, followed by dissolution of the silica core. In capsule dispersion, (1)H PFG echo decays of phenol are single exponentials, implying fast exchange of phenol between a free site and a capsule-bound site. However, apparent diffusion coefficients extracted from the echo decays depend on the diffusion time, which is typically not the case for the fast exchange limit. We attribute this to a particular regime, where apparent diffusion coefficients are observed, which arise from the signal of free phenol only but are influenced by exchange with molecules bound to the capsule, which exhibit a very fast spin relaxation. Indeed, relaxation rates of phenol are strongly enhanced in the presence of capsules, indicating binding to the capsule wall rather than encapsulation in the interior. We present a quantitative analysis in terms of a combined diffusion-relaxation model, where exchange times can be determined from diffusion and spin relaxation experiments even in this particular regime, where the bound site acts as a relaxation sink. The result of the analysis yields exchange times between free phenol and phenol bound to the capsule wall, which are on the order of 30 ms and thus slower than the diffusion controlled limit. From bound and free fractions an adsorption isotherm of phenol to the capsule wall is extracted. The binding mechanism and the exchange mechanism are discussed. The introduction of the global analysis of diffusion as well as relaxation echo decays presented here is of large relevance for adsorption dynamics in colloidal systems or other systems, where the standard diffusion echo decay analysis is complicated by rapidly relaxing boundary conditions.     

On the possibility of quantum beats in the total fluorescence of large molecules

The temporal evolution of the total emission from excited electronic states of a large molecule which corresponds to the statistical limit for radiationless relaxation is considered within the two-discrete-states model. It is shown that quantum beats in total (spectrally unresolved) emission may be revealed when the excited discrete levels differ in their rate constants for radiationless relaxation even if they have equal rate constants for radiative decay.     

Exploring the crystallinity of different powder sugars through solid echo and magic sandwich echo sequences

Time-domain nuclear magnetic resonance techniques are frequently used in polymer, pharmaceutical, and food industries as they offer rapid experimentation and generally do not require any considerable preliminary sample preparation. Detection of solid and liquid fractions in a sample is possible with the free induction decay (FID). However, for the classical FID sequence that consists of a single pulse followed by relaxation decay acquisition, the dead time of the probe (ring out of resonance circuitry) occurs and varies between 5 and 15 μs for standard 10-mm tubes. In such a case, there arises a risk that the signal from the solid fraction cannot be detected correctly. To obtain quantitative measurement on crystalline and more mobile amorphous fractions, alternative sequences to the classical FID in the solid-state nuclear magnetic resonance were developed. Solid echo and magic sandwich echo sequences perform the relaxation decay refocusing somehow excluding the dead time problem and allow detection of the signal from the solid fraction. In this study, knowledge of amorphous/crystal fraction, which is obtained through solid echo and magic sandwich echo, has been explored on powder sugar samples for the purpose of developing a groundwork for a reliable quality control method. Different sugars were examined for the utilization of the sequences. What is important to add and make this study unique is that the method proposed did not involve multiparameter fitting of the “bead” pattern FID signal that normally suffers from ambiguity; just the integration of the fast Fourier transform of the solid echo was needed to calculate the second moment, (M₂).     

The effects of annealing in inert atmospheres and of oxygen concentration on chemiluminescence from polypropylene

It has been shown that heating polypropylene powder under a nitrogen atmosphere leads to the significant prolongation of the oxidation induction time measured by chemiluminescence in oxygen at 130 and 140 °C. While heating in nitrogen from 0 to 4 h at 140 °C leads to the linear increase of oxidation induction time, the maximum chemiluminescence intensity I_stat increases with the time of sample annealing until 2 h; then it starts to decay. The different and sometime unknown thermal history of the sample may thus explain the scatter of induction times of oxidation observed with different PPs whether they be pure or stabilised. Maximum chemiluminescence intensity plotted vs. concentration of oxygen in the surrounding atmosphere at 130 and 140 °C also increases linearly; however, this does not correspond with very small reduction of oxidation induction time. The four-parametric “master equations” used in our earlier papers were applied to fit the chemiluminescence runs both in oxygen and in nitrogen. The equation operates with the rate constants of hydroperoxide decomposition and oxidation spreading but at the same time, it takes into account the possible effect of oxidation products on decomposition of hydroperoxides.     

Hidden Relaxation Channels in Aqueous Methylene Blue after Functionalization of Graphene Oxide Probed by Transient Absorption Spectroscopy

The mixture of graphene oxide (GO) and dye molecules may provide some new applications due to unique electronic, optical, and structural properties. Methylene blue (MB), a typical anionic dye, can attach on GO via π-π stacking and electrostatic interaction, and the molecule removal process on GO has been observed. However, it remains unclear about the ultrafast carrier dynamics and the internal energy transfer pathways of the system which is composed of GO and MB. We have employed ultrafast optical pump-probe spectroscopy to investigate the excited dynamics of the GO-MB system dispersed in water by exciting the samples at 400 nm pump pulse. The pristine MB and GO dynamics are also analyzed in t_andem for a direct comparison. Utilizing the global analysis to fit the measured signal via a sequential model, five lifetimes are acquired:(0.61±0.01) ps, (3.52±0.04) ps, (14.1±0.3) ps, (84±2) ps, and (3.66±0.08) ns. The ultrafast dynamics corresponding to these lifetimes was analyzed and the new relaxation processes were found in the GO-MB system, compared with the pristine MB. The results reveal that the functionalization of GO can alter the known decay pathways of MB via the energy transfer from GO to MB in system, the increased intermediate state, and the promoted energy transfer from triplet state MB to ground state oxygen molecules dissolved in aqueous sample.     

Global Analysis of Correlation Functions: Dynamic Light Scattering from Polymers and Block Copolymers

Dynamic light scattering has become a standard technique for investigating colloidal suspensions, polymer solutions, melts, blends, gels and other more complex systems. The experimental field autocorrelation function ĝ_l(t) can often be well modeled by a Laplace transform relating ĝ_l(t) to a distribution of decay times A(tau). In simple systems, A(τ) can usually be directly related to a distribution of molecular weights, particle sizes, diffusion coefficients, relaxation times or other physically relevant quantities. With constrained regularization methods, the parameter‐free estimation of A(τ) has become straightforward. In complex systems, the resulting A(τ) may contain several components the identification of which is not always obvious. The problem often originates in a superposition of components that have different variations of the decay time with the scattering vector. We present the method based on a simultaneous fit of several autocorrelation fuctions (ACF) measured at several different scattering angles, which, using simple and reasonable assumptions, yields a robust analysis of the spectra of decay times. The application of the method is illustrated on simulated autocorrelation functions as well as on real experimental data obtained on a variety of polymer systems.