Deprotonation dynamics and stokes shift of pyranine (HPTS)

The short and intermediate time scale dynamics of the photoacid pyranine (1-hydroxy-3,6,8-pyrenetrisulfonic acid, commonly referred to as HPTS) are studied with visible pump-probe spectroscopy in various solvents to elucidate the nature of its proton-transfer kinetics in water. The observed time dependences of HPTS are compared with those of the methoxy derivative, MPTS. A global fitting procedure is employed to model both the spectral shift (Stokes shift) caused by solvent reorganization and deprotonation of pyranine in water. Three distinct time-dependent features can be clearly identified. They are the Stokes shift (1 ps in H(2)O and 1.5 ps in D(2)O), followed by the deprotonation processes, which gives rise to a biexponential decay of the protonated species with time constants (in H(2)O) of 3 and 88 ps. By the use of a model previously discussed in the literature, the biexponential process can be interpreted as an initial deprotonation step followed by the longer time scale process which separates the resulting ion pair. The results presented here are consistent with some of the previous reports but unambiguously identify and quantitatively measure the Stokes shift as a separate and distinct phenomenon from the deprotonation process, in contrast to other reports that have suggested that all short time (a few picoseconds) dynamics are merely a Stokes shift.     

The vibrational Stokes shift of water (HOD in D2O)

The vibrational Stokes shift of the OH stretching transition nu(OH) of water is the shift between the ground-state absorption and the excited-state (v=1) emission. A recent measurement on HOD in D(2)O solvent [S. Woutersen and H. J. Bakker, Phys. Rev. Lett. 83, 2077 (1999)] of a 70 cm(-1) redshift, and a subsequent calculation of a 57 cm(-1) redshift using equilibrium molecular dynamics simulations [C. P. Lawrence and J. L. Skinner, J. Chem. Phys. 117, 8847 (2002)] were in good agreement. We now report extensive measurements of the vibrational Stokes shift in HOD/D(2)O using an ultrafast IR pump, Raman probe method. The vibrational Stokes shift is seen to depend on the pump pulse frequency and on time delay; by varying these parameters it can be made to range from 112 to -32 cm(-1) (negative values indicate a blueshift in the excited state). The equilibrium vibrational Stokes shift is actually a negative rather than a positive quantity. Possible reasons for the disagreement between experiment and theory are briefly discussed.     

Measurement of solvation responses at multiple sites in a globular protein

Proteins respond to electrostatic perturbations through complex reorganizations of their charged and polar groups, as well as those of the surrounding media. These solvation responses occur both in the protein interior and on its surface, though the exact mechanisms of solvation are not well understood, in part because of limited data on the solvation responses for any given protein. Here, we characterize the solvation kinetics at sites throughout the sequence of a small globular protein, the B1 domain of streptococcal protein G (GB1), using the synthetic fluorescent amino acid Aladan. Aladan was incorporated into seven different GB1 sites, and the time-dependent Stokes shift was measured over the femtosecond to nanosecond time scales by fluorescence upconversion and time-correlated single photon counting. The seven sites range from buried within the protein core to fully solvent-exposed on the protein surface, and are located on different protein secondary structures including beta-sheets, helices, and loops. The dynamics in the protein sites were compared against the free fluorophore in buffer. All protein sites exhibited an initial, ultrafast Stokes shift on the subpicosecond time scale similar to that observed for the free fluorophore, but smaller in magnitude. As the probe is moved from the surface to more buried sites, the dynamics of the solvation response become slower, while no clear correlation between dynamics and secondary structure is observed. We suggest that restricted movements of the surrounding protein residues give rise to the observed long time dynamics and that such movements comprise a large portion of the protein's solvation response. The proper treatment of dynamic Stokes shift data when the time scale for solvation is comparable to the fluorescence lifetime is discussed.     

Computer simulations of the solvation dynamics of Coumarin 153 in dimethylsulfoxide

We report molecular dynamics (MD) simulations of the solvation dynamics of Coumarin 153 in liquid dimethylsulfoxide using two distinct sets of partial charges for the coumarin probe. The excited state dipole moment of the coumarin and the dynamic Stokes shift in solution depend significantly on the type of charge distributions used. Nevertheless, the overall characteristics of the solvation responses obtained from both sets of charges are very similar and show good agreement with time-dependent Stokes shift experiments. Microscopic details of the solvent reorganization around the probe are discussed in light of the charge transfer upon photoexcitation.     

Solvent response and dielectric relaxation in supercooled butyronitrile

We have measured the dynamics of solvation of a triplet state probe, quinoxaline, in the glass-forming dipolar liquid butyronitrile near its glass transition temperature T(g)=95 K. The Stokes shift correlation function displays a relaxation time dispersion of considerable magnitude and the optical linewidth changes along the solvation coordinate in a nonmonotonic fashion. These features are characteristic of solvation in viscous solvents and clearly indicate heterogeneous dynamics, i.e., spatially distinct solvent response times. Using the dielectric relaxation data of viscous butyronitrile as input, a microscopic model of dipolar solvation captures the relaxation time, the relaxation dispersion, and the amplitude of the dynamical Stokes shift remarkably well.     

Theory of the time development of the stokes shift in polar media

We present a theory for the time evolution of the Stokes shift of a polar molecule in a polar solvent. The time-dependent solute—solvent interaction is calculated in a continuum model by replacing the surrounding solvent by a frequency-dependent dielectric continuum. An expression for the time dependence of the fluorescence maximum is derived. This expression can be considered a direct generalization of the well-known Ooshika—Lippert—Mataga equation to the time domain. We also present an approximate expression for the wavelength dependence of the dynamics of the Stokes shift, and find it to be consistent with recent experimental results. We have investigated the effect of polarizability of the solute molecule and found that for many molecules this effect is not negligible.     

Hydration dynamics and time scales of coupled water-protein fluctuations

We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior. Further constrained MD simulations with either frozen protein or frozen water revealed the molecular mechanism of slow hydration processes and elucidated the role of protein fluctuations. Observation of slow water dynamics in MD simulations requires protein flexibility, regardless of whether the slow Stokes shift component results from the water or protein contribution. The initial dynamics in a few picoseconds represents fast local motions such as reorientations and translations of hydrating water molecules, followed by slow relaxation involving strongly coupled water-protein motions. We observed a transition from one isomeric protein configuration to another after 10 ns during our 30 ns ground-state simulation. For one isomer, the surface hydration energy dominates the slow component of the total relaxation energy. For the other isomer, the slow component is dominated by protein interactions with the chromophore. In both cases, coupled water-protein motion is shown to be necessary for observation of the slow dynamics. Such biologically important water-protein motions occur on tens of picoseconds. One significant discrepancy exists between theory and experiment, the large inertial relaxation predicted by simulations but clearly absent in experiment. Further improvements required in the theoretical model are discussed.     

Solvation dynamics in protein environments: comparison of fluorescence upconversion measurements of coumarin 153 in monomeric hemeproteins with molecular dynamics simulations

The complexes of the fluorescence probe coumarin 153 with apomyoglobin and apoleghemoglobin are used as model systems to study solvation dynamics in proteins. Time-resolved Stokes shift experiments are compared with molecular dynamics simulations, and very good agreement is obtained. The solvation of the coumarin probe is very rapid with approximately 60% occurring within 300 fs and is attributed to interactions with water (or possibly to the protein itself). Differences in the solvation relaxation (or correlation) function C(t) for the two proteins are attributed to differences in their hemepockets.     

第一性原理研究LuAlO3中掺杂Ce3+的4f-5d跃迁性质

We have investigated properties of the compound LuAlO₃:Ce³⁺ associated with the Ce³⁺ 4f-5d transition by using the periodic density functional theory. A hybrid functional has been used for the 4f states and a constrained approach has been employed for the excited 5d state. It is found that the average distance between Ce³⁺ and the eight nearest-neighbor O atoms decrease by 0.05 ?on going from 4f to 5d state. The calculated Stokes shift is in good agreement with experiment. Based on the optimized structure around Ce³⁺, the energy level scheme of the 5d states has been evaluated using the angular overlap model, in reasonable agreement with experiment.     

Characterization of the solvation dynamics of an ionic liquid via molecular dynamics simulation

The solvation dynamics of ionic liquids have been the subject of intense experimental study but remain poorly understood. We present the results of molecular dynamics simulations of the solvation dynamics of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate in response to photoexcitation of the fluorescent dye coumarin-153. We reproduce the time-resolved fluorescence Stokes shift using linear response theory, then use novel statistical techniques to analyze cation and anion contributions to the signal. We find that the solvation dynamics are dominated by collective ionic motion and characterize the time scale for various features of the collective response. Further, we use the Steele analysis [Mol. Phys. 61, 1031 (1987)] to characterize the contributions to the observed Stokes shift made by translational and rovibrational degrees of freedom. Our results indicate that in contrast to molecular liquids, the rovibrational response is trivial and the observed fluorescence response arises almost entirely from ionic translation. Our results resolve previously open questions in the literature about the nature of the rapid dynamics in room-temperature ionic liquids and offer insight into the physical principles governing ionic liquid behavior on longer time scales.     

Zinc complexes of 1-Propyl-2-(2-tosylaminophenyl)-5-aminobenzimidazole: Synthesis,structure, and luminescence properties

1-Alkyl-2-(2-tosylaminophenyl)-5-aminobenzimidazole and related zinc complexes are synthesized. The structure of the complex with zinc pivalate is determined by X-ray diffraction analysis. The fluorescence with the anomalous Stokes shift of the benzimidazole ligand system in solution is transformed into the fluorescence with the normal Stokes shift upon complex formation due to blocking the mechanism of intramolecular proton transfer in the excited state or upon the transition to the crystalline state formed by zwitterionic forms that are generated due to the proton transfer from the sulfonamide group to the amino group.     

Probing polar solvation dynamics in proteins: a molecular dynamics simulation analysis

Measurements of time-resolved Stokes shifts on picosecond to nanosecond time scales have been used to probe the polar solvation dynamics of biological systems. Since it is difficult to decompose the measurements into protein and solvent contributions, computer simulations are useful to aid in understanding the details of the molecular behavior. Here we report the analysis of simulations of the electrostatic interactions of the rest of the protein and the solvent with 11 residues of the immunoglobulin binding domain B1 of protein G. It is shown that the polar solvation dynamics are position-dependent and highly heterogeneous. The contributions due to interactions with the protein and with the solvent are determined. The solvent contributions are found to vary from negligible after a few picoseconds to dominant on a scale of hundreds of picoseconds. The origin for the latter is found to involve coupled hydration and protein conformational dynamics. The resulting microscopic picture demonstrates that a wide range of possibilities have to be considered in the interpretation of time-resolved Stokes shift measurements.     

Time-dependent fluorescence in nanoconfined solvents: linear-response approximations and Gaussian statistics

The time-dependent fluorescence of a model dye molecule in a nanoconfined solvent is used to test approximations based on the dynamic and static linear-response theories and the assumption of Gaussian statistics. Specifically, the results of nonequilibrium molecular-dynamics simulations are compared to approximate expressions involving time correlation functions obtained from equilibrium simulations. Solvation dynamics of a model diatomic dye molecule dissolved in acetonitrile confined in a spherical hydrophobic cavity of radius 12, 15, and 20 A? is used as the test case. Both the time-dependent fluorescence energy, expressed as the normalized dynamic Stokes shift, and the time-dependent position of the dye molecule after excitation are examined. While the dynamic linear-response approximation fails to describe key aspects of the solvation dynamics, assuming Gaussian statistics reproduces the full nonequilibrium simulations well. The implications of these results are discussed.     

Approaches to the solvation of the molecular probe N-methyl-6-quinolone in its excited state

The molecular probe N-methyl-6-quinolone (MQ) gives experimental access to its local chemical environment, e.g. inside a biomolecule. Using ab initio molecular dynamics (MD), it is possible to simulate the time evolution of the Stokes shift as a function of the actual atomistic coupling to the surrounding hydrogen bond network and thus obtain a comprehensive view of the local environment. In contrast to ground state ab initio MD simulations, the choice of a method for excited state MD is nontrivial. Here, we develop a simple and accurate model for the solvation dynamics of MQ in its first excited state.     

Intrachain photoluminescence dynamics of MEH-PPV in the solid state

The photoluminescence (PL) dynamics of poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) blended in host polymer (polypropylene, PP) matrix as well as that in the neat film has been studied. The concentration of MEH-PPV in the PP blend is designed to be fairly low (0.01 wt %) in order to observe the intrinsic intrachain PL property of MEH-PPV in the solid state. The steady-state 0-0 PL band of the blend sample shows a blue-shift of 0.12 eV with respect to that of the neat film of MEH-PPV. The PL-excitation (PLE) spectra of the blend sample exhibit definite vibronic structure, and hence we can determine the magnitude of the Stokes shift as 0.06 eV. The blend sample shows a single-exponential PL decay at 4 K with a time constant of 850 ps. We emphasize that this single-exponential-type PL decay is an intrinsic property of the intrachain PL species. Time-resolved PL measurements confirm dynamical red-shift of the PL band in the neat film, whereas this trend is not found in the case of the PP blend. These observations indicate that the energy transfer between finite segments, which can cause exciton migration, is much less efficient within the isolated MEH-PPV polymer chain compared to the case of the interchain transfer. The time-resolved measurements further demonstrate that the Stokes shift identified in the blend sample takes place at the early stage within 50 ps following photoexcitation. We attribute this Stokes shift to the rapid increase of the planarity of the MEH-PPV chain caused by the torsion of some constituent phenyl rings following photoexcitation. Finally, based on an argument on the different magnitudes of Stokes shift between the blend sample and the neat film, we conclude that the PL of MEH-PPV in the neat film predominantly occurs at the site of interchain excitations via the interchain migration of excitons.     

Artificial cytochrome b: computer modeling and evaluation of redox potentials.

We generated atomic coordinates of an artificial protein that was recently synthesized to model the central part of the native cytochrome b (Cb) subunit consisting of a four-helix bundle with two hemes. Since no X-ray structure is available, the structural elements of the artificial Cb were assembled from scratch using all known chemical and structural information available and avoiding strain as much as possible. Molecular dynamics (MD) simulations applied to this model protein exhibited root-mean-square deviations as small as those obtained from MD simulations starting with the crystal structure of the native Cb subunit. This demonstrates that the modeled structure of the artificial Cb is relatively rigid and strain-free. The model structure of the artificial Cb was used to determine the redox potentials of the two hemes by calculating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation (LPBE). The calculated redox potentials agree within 20 meV with the experimentally measured values. The dependence of the redox potentials of the hemes on the protein environment was analyzed. Accordingly, the total shift in the redox potentials is mainly due to the low dielectric medium of the protein, the protein backbone charges, and the salt bridges formed between the arginines and the propionic acid groups of the hemes. The difference in the shift of the redox potentials is due to the interactions with the hydrophilic side chains and the salt bridges formed with the propionic acids of the hemes. For comparison and to test the computational procedure, the redox potentials of the two hemes in the native Cb from the cytochrome bc(1) (Cbc(1)) complex were also calculated. Also in this case the computed redox potentials agree well with experiments.     

Nanocrystals for large Stokes shift-based optosensing

The influence of Stokes shift in optosensing was discussed. Then, the current status of large Stokes shift-based optosensing was reviewed here.     

Nanocrystals for large Stokes shift-based optosensing

Stokes shift is an important feature of fluorescence, which reveals the energy loss between the excitation and the emission. For most fluorescent materials(e.g., organic dyes and proteins), the large overlap between the absorption and emission spectra endow them a small Stokes shift that induced reabsorption by fluorophore itself. Although the self-absorption can be effectively reduced due to the emergence of fluorescent nanomaterials, fluorescence attenuation is still observed in aggregated or concentrated nanocrystals, causing reduced sensitivity of biosensors. Therefore, increasing the Stokes shift can effectively improve the performance of nano-agents based biosensing. In this critical review, through understanding the Stokes shift from the viewpoint of self-absorption, the influence of Stokes shift on fluorescence properties are discussed. Based on the principle of changing the Stokes shift of fluorescent nanomaterials, we described the methods for constructing various optically large Stokes shift-based nanomaterials, and the application of these nanocrystals in biosensing is especially concerned in this review.     

丁烷衍生物类木脂素13C NMR化学位移预测

借助原子电性作用矢量(AEIV)和原子杂化状态指数(AHSI),对39种丁烷衍生物类木脂素共计854个等价C原子进行表征,并建立用于模拟该类分子13C NMR化学位移的多元线性回归方程.所得定量结构波谱关系(QSSR)模型及留一法交互检验相关系数分别为r=0.981和q=0.962.进一步用从马尾松松针中分离所得新木脂素中20个13C NMR化学位移对模型进行外部验证,预测结果与实验值较接近.表明所建模型有良好稳定性和泛化力,可对丁烷衍生物类木脂素13C NMR谱学数据准确模拟.