N-乙基丙酰胺的飞秒二维红外光谱

利用飞秒二维红外实验方法, 结合稳态红外光谱实验和计算化学手段, 对β-肽模型分子N-乙基丙酰胺(NEPA)的超快结构动力学进行了研究. 结果表明, 在水溶液中, NEPA具有类α-肽酰胺-I 带的振动特征, 并表现出对分子结构和化学环境的灵敏性. 二维红外光谱动力学结果揭示了一个1 ps 左右的光谱扩散时间, 与酰胺-水之间的氢键结构动力学时间尺度一致.     

Water-protein interactions in microcrystalline crh measured by 1H-13C solid-state NMR spectroscopy

Using solid-state NMR carbon-proton dipolar correlation spectroscopy, we observed hydrogen exchange on the millisecond time scale between water molecules and protein protons in a solid sample. These interactions are shown to be related to important structural features of the protein such as hydrogen-bonding or salt-bridge networks.     

Conformational dynamics of bistable RNAs studied by time-resolved NMR spectroscopy

The structural transition between two alternate conformations of bistable RNAs has been characterized by time-resolved NMR spectroscopy. The mechanism, kinetics, and thermodynamics underlying the global structural transition of bistable RNAs were delineated. Both bistable RNA conformations and a partial unstructured RNA of identical sequence could be trapped using photolabile protecting groups. This trapping allowed for an investigation of the initial folding from an unfolded RNA to one of the preferred conformations of the bistable RNA and of the structural transitions involved. Folding of the secondary structure elements occurs rapidly, while the global structural transition of the bistable RNA occurs on a time scale of minutes and shows marked temperature dependence. Comparison of these results with bistable systems previously investigated leads to the prediction of activation enthalpies (DeltaH++) associated with global structural transitions in RNA.     

Structural ordering in glass forming tellurium-germanium melts

The character of reorganization of the short-range order and the scale structure during the ordering of glass forming melts is elaborated based on the results of diffraction and microscopic investigations of the ordered and glassy alloys in tellurium-germanium systems. For this purpose cooling curves reflecting the formation processes of structural levels in real time are analyzed and the effective activation energies are estimated.     

Photoinduced bimolecular electron transfer investigated by femtosecond time-resolved infrared spectroscopy

Ultrafast infrared transient absorption spectroscopy is used to study the photoinduced bimolecular electron transfer reaction between perylene in the first singlet excited state and 1,4-dicyanobenzene in acetonitrile and dichloromethane. Following vibrational marker modes on both donor and acceptor sides in real time provides direct insight into the structural dynamics during the reaction. A band narrowing on a time scale of a few tens of picoseconds observed on the antisymmetric CN stretching vibration of the dicyanobenzene radical anion indicates that a substantial part of the excess energy is channeled into vibrational modes of the product, despite the fact that the reaction is weakly exergonic. An additional narrowing of the same band on a time scale of several hundreds of picoseconds observed in acetonitrile only is interpreted as a signature of the dissociation of the geminate ion pairs into free ions.     

Ultrafast structural dynamics of water induced by dissipation of vibrational energy

In the liquid phase, water molecules form a disordered fluctuating network of intermolecular hydrogen bonds. Using both inter- and intramolecular vibrations as structural probes in ultrafast infrared spectroscopy, we demonstrate a two-stage structural response of this network to energy disposal: vibrational energy from individually excited water molecules is transferred to intermolecular modes, resulting in a sub-100 fs nuclear rearrangement that leaves the local hydrogen bonds weakened but unbroken. Subsequent energy delocalization over many molecules occurs on an approximately 1 ps time scale and is connected with the breaking of hydrogen bonds, resulting in a macroscopically heated liquid.     

Communication: Fast and local predictors of the violation of the Stokes-Einstein law in polymers and supercooled liquids

The violation of the Stokes-Einstein (SE) law is investigated in a melt of linear chains by extensive molecular-dynamics simulations. It is found that the SE breakdown is signaled (with 5% uncertainty) by the monomer mean-square displacement on the picosecond time scale. On this time scale the displacements of the next-next-nearest neighbors are uncorrelated. It is shown that: (i) the SE breakdown occurs when is smaller than the breadth of the distribution of the square displacements to escape from the first-neighbors cage, (ii) the dynamical heterogeneity affects the form of the master curve of the universal scaling between the structural relaxation and .     

A polymer in an ionic liquid: Structural properties of a system during attraction between the polymer and cations of the ionic liquid

In terms of the polymer integral equation theory, structuring in ionic liquids containing flexiblechain polymers under the conditions of good solubility is studied for the first time. The influence of the polymer concentration on the structural properties of system components is studied at different lengths of polymer molecules. The structural organization of the ionic liquids is shown to be fairly stable after addition of the polymer. When there is attraction between the polar groups of cations of the ionic liquid and polymer molecules, the calculated structural factors suggest intermediate-range scales of polymer-component ordering. Given this, for any considered length of polymer molecules, there is a range of polymer concentrations in which the characteristic scale of ordering decreases with an increase in polymer density according to a power law.     

Backbone motions of free and pheromone-bound major urinary protein I studied by molecular dynamics simulation

Molecular motions of free and pheromone-bound mouse major urinary protein I, previously investigated by NMR relaxation, were simulated in 30 ns molecular dynamics (MD) runs. The backbone flexibility was described in terms of order parameters and correlation times, commonly used in the NMR relaxation analysis. Special attention was paid to the effect of conformational changes on the nanosecond time scale. Time-dependent order parameters were determined in order to separate motions occurring on different time scales. As an alternative approach, slow conformational changes were identified from the backbone torsion angle variances, and "conformationally filtered" order parameters were calculated for well-defined conformation states. A comparison of the data obtained for the free and pheromone-bound protein showed that some residues are more rigid in the bound form, but a larger portion of the protein becomes more flexible upon the pheromone binding. This finding is in general agreement with the NMR results. The higher flexibility observed on the fast (fs-ps) time scale was typically observed for the residues exhibiting higher conformational freedom on the ns time scale. An inspection of the hydrogen bond network provided a structural explanation for the flexibility differences between the free and pheromone-bound proteins in the simulations.     

Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy

Spectrally resolved infrared stimulated vibrational echo spectroscopy is used to measure the fast dynamics of heme-bound CO in carbonmonoxy-myoglobin (MbCO) and -hemoglobin (HbCO) embedded in silica sol-gel glasses. On the time scale of approximately 100 fs to several picoseconds, the vibrational dephasing of the heme-bound CO is measurably slower for both MbCO and HbCO relative to that of aqueous protein solutions. The fast structural dynamics of MbCO, as sensed by the heme-bound CO, are influenced more by the sol-gel environment than those of HbCO. Longer time scale structural dynamics (tens of picoseconds), as measured by the extent of spectral diffusion, are the same for both proteins encapsulated in sol-gel glasses compared to that in aqueous solutions. A comparison of the sol-gel experimental results to viscosity-dependent vibrational echo data taken on various mixtures of water and fructose shows that the sol-gel-encapsulated MbCO exhibits dynamics that are the equivalent of the protein in a solution that is nearly 20 times more viscous than bulk water. In contrast, the HbCO dephasing in the sol-gel reflects only a 2-fold increase in viscosity. Attempts to alter the encapsulating pore size by varying the molar ratio of silane precursor to water (R value) used to prepare the sol-gel glasses were found to have no effect on the fast or steady-state spectroscopic results. The vibrational echo data are discussed in the context of solvent confinement and protein-pore wall interactions to provide insights into the influence of a confined environment on the fast structural dynamics experienced by a biomolecule.     

Introduction of a new scale into reversed-phase high-performance liquid chromatography of pyridylamino sugar chains for structural assignment

Addition of a monosaccharide residue to a pyridylaminated (PA)-N-linked sugar chain results in an increment or decrement in the elution time on reversed-phase HPLC, the difference being defined as the partial elution time of the residue. Based on this principle, an empirical rule was deduced, which states that the elution time is roughly equal to the sum of the partial elution times of the component sugar residues [Anal. Biochem., 167 (1987) 321–326]. In practice, however, some partial elution times obtained from different pairs of mother PA-sugar chains are found to deviate, and consequently the closeness of the elution times of PA-sugar chains calculated therefrom to the observed times is reduced in such cases. To improve the reliability of the additivity rule and to generalize elution times so that they are less dependent on minor alterations in the elution conditions, we have devised a new scale for elution time, which we have named a reversed-phase scale. The elution times on the reversed-phase scale (the R values) are read from a conversion curve constructed using the elution times of eight selected standard PA-sugar chains. The partial elution times on the reversed-phase scale of 22 monosaccharide residues were calculated from the R values of 93 PA-sugar chains. The R values obtained by summing the partial elution times of all the component monosaccharide residues became much closer to the R values obtained from the reversed-phase scale, compared to the results obtained using the previous method. In addition, the R values were less influenced by minor change in the elution conditions. These features of the new scale allow more accurate structural assignment of sugar chains.     

2-Trifluoromethyl-1,3-dithianylium triflate: a convenient ‘masked’ electrophilic pentafluoroethylation reagent

With 2-trifluoromethyl-1,3-dithianylium triflate for the first time the synthesis, isolation and full structural characterization of an α-perfluoroalkylcarbenium salt was achieved. The title compound can be easily obtained on a preparative scale. The thermally stable dithianylium salt in combination with fluorodesulfurization chemistry is a promising novel reagent for the electrophilic polyfluoroalkylation of organic substrates, demonstrated by the pentafluoroethylation of O-nucleophiles.     

Multi-Dimensional Structure and Dynamics Landscape of Proteins in Mammalian Cells Revealed by In-Cell NMR

Governing function, half-life and subcellular localization, the 3D structure and dynamics of proteins are in nature constantly changing in a tightly regulated manner to fulfill the physiological and adaptive requirements of the cells. To find evidence for this hypothesis, we applied in-cell NMR to three folded model proteins and propose that the splitting of cross peaks constitutes an atomic fingerprint of distinct structural states that arise from multiple target binding co-existing inside mammalian cells. These structural states change upon protein loss of function or subcellular localisation into distinct cell compartments. In addition to peak splitting, we observed NMR signal intensity attenuations indicative of transient interactions with other molecules and dynamics on the microsecond to millisecond time scale.     

Ultrafast energy transfer and structural dynamics in DNA

Ultrafast structural dynamics concomitant to excitation energy transfer in DNA has been studied using a pair of pyrene-labeled DNA bases. The temporal evolution of the femtosecond pump-probe spectra reveals the existence of two electronic coupling pathways, through-base stack and through-space, which lead to excitation energy transfer and excimer formation even when the labeled DNA bases are separated by one AT base pair. The electronic coupling which mediates through-base stack energy transfer is so strong that a new absorption band arises in the excited-state absorption spectrum within 300 fs. From the analysis of time-dependent spectral shifts due to through-space excimer formation, the local structural dynamics and flexibility of DNA are characterized on the picosecond and nanosecond time scale.     

Time-resolved,static light scattering: New possibilities in polymer characterization

We have developed a highly sensitive, multi-angle, static light scattering (TRSLS = time resolved static light scattering) instrument, which measures the angular dependent Rayleigh scattering intensity of solutions simultaneously at 38 angles within approximately one second. It is thus suitable as a quick and easy to use static light scattering device for routine polymer and colloid characterization. The time resolution allows the kinetics of many systems to be investigated down to a second time scale, such as polymerization kinetics of linear, branched and crosslinked polymer structures, thermoreversible gelation, growth of colloidal particles, structural changes in micellar systems, etc.     

EIS characterization of the evolution of calcium carbonate scaling in cooling systems in presence of inhibitors

Electrochemical impedance spectroscopy (EIS) was used to assess the relative effects of scaling and corrosion for steel electrodes in cooling water media and to obtain information on corrosion inhibition and scale inhibition properties of 1-hydroxyethylidene-1,1-diphosphonic acid (HEDP) and hydroxyphosphonoacetic acid (HPA). Steel electrodes were preliminary scaled with CaCO₃ in simulated cooling water and then immersed in the characterization solution. Analysis of the impedance spectra with a simple model allowed following of the time evolution of physical parameters corresponding to the calcium carbonate islands and to the corrosion products accumulated in areas not covered by the scale. In uninhibited solutions, the main effect was the progressive deposit of corrosion products with no additional scaling and little restructuring of the initial carbonate islands. When the solution contained HEDP alone, part of the initial scale was detached from the surface, but the presence of HPA or the mixture HPA+HEDP only induced structural modifications of the initial scale. Moreover, the impedance analysis also showed that HPA exhibited better corrosion inhibition properties than HEDP.     

100 Picosecond Diffraction Catches Structural Transients of Laser‐Pulse Triggered Switching in a Spin‐Crossover Crystal

We study by 100 picosecond X‐ray diffraction the photo‐switching dynamics of single crystal of the orthorhombic polymorph of the spin‐crossover complex [(TPA)Fe(TCC)]PF₆, in which TPA=tris(2‐pyridyl methyl)amine, TCC^2?=3,4,5,6‐Cl₄‐Catecholate^2?. In the frame of the emerging field of dynamical structural science, this is made possible by using optical pump/X‐ray probe techniques, which allow following in real time structural reorganization at intra‐ and intermolecular levels associated with the change of spin state in the crystal. We use here the time structure of the synchrotron radiation generating 100 picosecond X‐ray pulses, coupled to 100 fs laser excitation. This study has revealed a rich variety of structural reorganizations, associated with the different steps of the dynamical process. Three consecutive regimes are evidenced in the time domain: 1) local molecular photo‐switching with structural reorganization at constant volume, 2) volume relaxation with inhomogeneous distribution of local temperatures, 3) homogenization of the crystal in the transient state 100 µs after laser excitation. These findings are fundamentally different from those of conventional diffraction studies of long‐lived photoinduced high spin states. The time‐resolution used here with picosecond X‐ray diffraction probes different physical quantities on their intrinsic time‐scale, shedding new light on the successive processes driving macroscopic switching in a functionalized material. These results pave the way for structural studies away from equilibrium and represent a first step toward femtosecond crystallography.     

Communication: correlation of the instantaneous and the intermediate-time elasticity with the structural relaxation in glassforming systems

The elastic models of the glass transition relate the increasing solidity of the glassforming systems with the huge slowing down of the structural relaxation and the viscous flow. The solidity is quantified in terms of the instantaneous shear modulus G(∞), i.e., the immediate response to a step change in the strain. By molecular-dynamics simulations of a model polymer system, one shows the virtual absence of correlations between the instantaneous elasticity and the structural relaxation. Instead, a well-defined scaling is evidenced by considering the elastic response observed at intermediate times after the initial fast stress relaxation. The scaling regime ranges from sluggish states with virtually pure elastic response on the picosecond time scale up to high-mobility states where fast restructuring events are more apparent.     

Diffusional anomaly and network dynamics in liquid silica

The present study applies the power spectral analysis technique to understand the diffusional anomaly in liquid silica, modeled using the Beest-Kramer-van Santen (BKS) potential. Molecular-dynamics simulations have been carried out to show that power spectrum of tagged particle potential energy of silica shows a regime with 1f(alpha) dependence on frequency f which is the characteristic signature of multiple time scale behaviour in networks. As demonstrated earlier in the case of water [J. Chem. Phys. 122, 104507 (2005)], the variations in the mobility associated with the diffusional anomaly are mirrored in the scaling exponent alpha associated with this multiple time scale behavior. Our results indicate that in the anomalous regime, as the local tetrahedral order decreases with temperature or pressure, the coupling of local modes to network reorganizations increases and so does the diffusivity. This symmetry-dependence of the vibrational couplings is responsible for the connection between the structural and diffusional anomalies.