基于位形熵模型的山梨醇玻璃焓松弛的量热分析

利用DSC技术考察了无定形山梨醇体系的焓松弛行为, 在10 K•min^－1的升温速率下测定了经历不同降温速率(0.5～20 K•min^－1)的山梨醇在玻璃化转变(T_g)前后的比热容[c_p(T)]. 利用基于位形熵演变的焓松弛现象学模型(GR模型)模拟了实验数据. 不论是否假设松弛过程存在一个亚稳极限态, 模型参数均能很好地重现经历不同热历史体系的升温c_p(T)曲线. 在物理意义明确的模型参数组中, 除了非指数参数随降温速率的增加而增加外, 其余均不随热历史的变化而变化. 拟合较低降温速率下c_p(T)曲线获得的GR模型参数的预测力明显好于在较大降温速率下获得的结果. 由于松弛时间对拟合过程中选择的“固定参数”的取值很敏感, 因此模型能否预测体系的比热容不能看成确定松弛时间的唯一依据. 在利用GR模型分析无定形山梨醇体系的脆度时, 如果选择极限假想温度作为T_g, 会导致计算结果明显小于文献值.     

General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation

A general framework is presented for the interpretation of NMR relaxation data of proteins. The method, termed isotropic reorientational eigenmode dynamics (iRED), relies on a principal component analysis of the isotropically averaged covariance matrix of the lattice functions of the spin interactions responsible for spin relaxation. The covariance matrix, which is evaluated using a molecular dynamics (MD) simulation, is diagonalized yielding reorientational eigenmodes and amplitudes that reveal detailed information about correlated protein dynamics. The eigenvalue distribution allows one to quantitatively assess whether overall and internal motions are statistically separable. To each eigenmode belongs a correlation time that can be adjusted to optimally reproduce experimental relaxation parameters. A key feature of the method is that it does not require separability of overall tumbling and internal motions, which makes it applicable to a wide range of systems, such as folded, partially folded, and unfolded biomolecular systems and other macromolecules in solution. The approach was applied to NMR relaxation data of ubiquitin collected at multiple magnetic fields in the native form and in the partially folded A-state using MD trajectories with lengths of 6 and 70 ns. The relaxation data of native ubiquitin are well reproduced after adjustment of the correlation times of the 10 largest eigenmodes. For this state, a high degree of separability between internal and overall motions is present as is reflected in large amplitude and collectivity gaps between internal and overall reorientational modes. In contrast, no such separability exists for the A-state. Residual overall tumbling motion involving the N-terminal beta-sheet and the central helix is observed for two of the largest modes only. By adjusting the correlation times of the 10 largest modes, a high degree of consistency between the experimental relaxation data and the iRED model is reached for this highly flexible biomolecule.     

An ab initio investigation of the Buckingham birefringence of furan, thiophene, and selenophene in cyclohexane solution

Using a recently developed quadratic response methodology for the calculation of frequency-dependent third-order properties of molecules in solution, we investigate the Buckingham birefringence of furan, thiophene, and selenophene in cyclohexane solution. These systems are chosen since accurate experimental data are available, allowing for a direct comparison of experimental observations with our theoretical estimates. Our model for describing the solvent effects is based on a dielectric continuum approach for the solvent, and uses a molecule-shaped cavity. Our results show qualitatively different Buckingham constants and effective quadrupole centers calculated with and without the solvent, and only when the solvent is included are the qualitative trends observed experimentally reproduced. It is demonstrated that a significant part of this effect arises from the geometry relaxation of the molecules in the solvent.     

Nonmonotonic temperature dependence of heat capacity through the glass transition within a kinetic model

The heat capacity of a supercooled liquid subjected to a temperature cycle through its glass transition is studied within a kinetic model. In this model, the beta process is assumed to be thermally activated and described by a two-level system. The alpha process is described as a beta relaxation mediated cooperative transition in a double well. The overshoot of the heat capacity during the heating scan is well reproduced and is shown to be directly related to delayed energy relaxation in the double well. In addition, the calculated scan rate dependencies of the glass transition temperature T(g) and the limiting fictive temperature T(f) (L) show qualitative agreement with the known results. Heterogeneity is found to significantly reduce the overshoot of heat capacity. Furthermore, the frequency dependent heat capacity has been calculated within the present framework and found to be rather similar to the experimentally observed behavior of supercooled liquids.     

退火条件对山梨醇玻璃焓松弛参数的影响

采用差示扫描量热法(DSC)测定山梨醇样品经历不同时间(t_a)等温退火后, 以10 K·min^-1速率进行升温时玻璃化转变温度(T_g)前后的比热容(C_p(T)). 将Gómez Ribelles (GR)提出的一种基于构型熵的现象学模型用于描述山梨醇玻璃的焓松弛行为, 考察GR模型能否适用于小分子玻璃体系. 结果表明, 单组GR模型参数拟合的曲线均能较好重现对应热历史条件下的山梨醇体系的实验所得C_p(T)曲线, 尽管并未找到不随热历史而变的一组参数作为材料常数, 但与其它现象学模型应用于小分子玻璃时, 其模型参数都随热历史变化而变化的特点相比, GR模型的某些参数基本保持不变. 且在较长退火时间下拟合得到的模型参数普适性较好. 同经历连续降温的山梨醇相比, 等温退火过程得到的松弛极限态参数(δ)的平均值与T_g处比热容增量(ΔC_p(T_g))的比值明显增大, 但仍小于聚合物的值, 表明GR模型提出的亚稳极限态对小分子玻璃的影响值得商榷.     

Relaxation and dephasing in open quantum systems time-dependent density functional theory: Properties of exact functionals from an exactly-solvable model system

The dissipative dynamics of many-electron systems interacting with a thermal environment has remained a long-standing challenge within time-dependent density functional theory (TDDFT). Recently, the formal foundations of open quantum systems time-dependent density functional theory (OQS-TDDFT) within the master equation approach were established. It was proven that the exact time-dependent density of a many-electron open quantum system evolving under a master equation can be reproduced with a closed (unitarily evolving) and non-interacting Kohn-Sham system. This potentially offers a great advantage over previous approaches to OQS-TDDFT, since with suitable functionals one could obtain the dissipative open-systems dynamics by simply propagating a set of Kohn-Sham orbitals as in usual TDDFT. However, the properties and exact conditions of such open-systems functionals are largely unknown. In the present article, we examine a simple and exactly-solvable model open quantum system: one electron in a harmonic well evolving under the Lindblad master equation. We examine two different representitive limits of the Lindblad equation (relaxation and pure dephasing) and are able to deduce a number of properties of the exact OQS-TDDFT functional. Challenges associated with developing approximate functionals for many-electron open quantum systems are also discussed.     

A new force field for atomistic simulations of aqueous tertiary butanol solutions

We present a new tert-butanol force field parametrized to reproduce the mixture thermodynamics of tert-butanol/water over a wide range of solution compositions at room temperature and atmospheric pressure. The experimental Kirkwood-Buff integrals, which quantify preferential solvation of solution components by the same species or by the other components, were used as target values to be reproduced. Water was modeled using the simple point charge model. In the range of alcohol mole fractions between 0.02 and 0.98, our optimized model satisfactorily reproduces alcohol-alcohol, water-water, and alcohol-water aggregation behavior. As a consequence, the solution activity derivatives are reproduced as well. A comparison has been made with solution activities obtained by free energy calculations (i.e., thermodynamic integration). It clearly shows that the Kirkwood-Buff based approach performs superior in predicting solution activities of liquid mixtures. The new tert-butanol model has been used to examine the solution structure and hydrophobic interactions in aqueous tert-butanol at the various mixture compositions. A comparison is made with structural data obtained by neutron diffraction.     

Absolute rates of hole transfer in DNA

Absolute rates of hole transfer between guanine nucleobases separated by one or two A:T base pairs in stilbenedicarboxamide-linked DNA hairpins were obtained by improved kinetic analysis of experimental data. The charge-transfer rates in four different DNA sequences were calculated using a density-functional-based tight-binding model and a semiclassical superexchange model. Site energies and charge-transfer integrals were calculated directly as the diagonal and off-diagonal matrix elements of the Kohn-Sham Hamiltonian, respectively, for all possible combinations of nucleobases. Taking into account the Coulomb interaction between the negative charge on the stilbenedicarboxamide linker and the hole on the DNA strand as well as effects of base pair twisting, the relative order of the experimental rates for hole transfer in different hairpins could be reproduced by tight-binding calculations. To reproduce quantitatively the absolute values of the measured rate constants, the effect of the reorganization energy was taken into account within the semiclassical superexchange model for charge transfer. The experimental rates could be reproduced with reorganization energies near 1 eV. The quantum chemical data obtained were used to discuss charge carrier mobility and hole-transport equilibria in DNA.     

Small-angle X-ray scattering study of photosystem I-detergent complexes: implications for membrane protein crystallization

Small-angle X-ray scattering (SAXS) was used to investigate the structure of isolated photosystem I (PSI) complexes stabilized in detergent solution. Two different types of PSI preparation were investigated. In the first preparation, thylakoid membranes were solubilized with Triton X100 and purified by density gradient centrifugation. SAXS data indicated large scattering objects or microphases that can be described as sheets with approximately 68 A thickness and a virtually infinite lateral extension. The observed thickness agreed well with the dimension of a PSI molecule across the thylakoid membrane. In the second preparation, PSI was isolated as before but was further purified by anion exchange chromatography resulting in functional complexes consisting of single PSI units with attached surfactant as evidenced by the particle volume and gyration radius extracted from the SAXS data. Several approaches were used to model the solution conformation of the complex. Three different ellipsoidal modeling approaches, a uniform density ellipsoid of revolution, a triaxial solid ellipsoid, and a core-shell model, found extended structures with dimensions that were not consistent with the PSI crystal structure (Ben-Shem, A.; et al. Nature 2003, 426, 630-635). Additionally, the SAXS data could not be modeled using the crystal structure embedded in a disk of detergent. The final approach considered the possibility that protein was partially unfolded by the detergent. The data were modeled using a "beads-on-a-string" approach that describes detergent micelles associated with the unfolded polypeptide chains. This model reproduced the position and relative amplitude of a peak present in the SAXS data at 0.16 A(-1) but was not consistent with the data at larger length scales. We conclude that the polypeptide subunits at the periphery of the PSI complex were partially unfolded and associated with detergent micelles while the catalytically active core of the PSI complex remained structurally intact. This interpretation of the solution structure of isolated PSI complexes has broader implications for the investigation of the interactions of detergents and protein, especially for crystallization studies.     

A comparison of Coulombic interaction methods in non-equilibrium studies of heat transfer in water

We investigate the impact of the treatment of electrostatic interactions on the heat conduction of liquid water. With this purpose, we report a series of non-equilibrium molecular dynamics computer simulations of the Modified Central Force Model of water. We consider both the Ewald summation approach, which includes the full range of the electrostatic interactions, and the Wolf method, which uses a cutoff to truncate the long range contributions. It is shown that the relaxation of the temperature profiles towards the stationary state solution and the equation of state of the liquid are not affected by the treatment of the electrostatic interactions. However, the truncation of the interactions results in lower internal energy fluxes as well as lower thermal conductivities. We also find that the anomalous increase of the thermal conductivity of water with temperature is reproduced by the different methods considered in this work, showing that this physical behavior is independent of the treatment of the long range electrostatic interactions.     

Analysis of infrared and microwave spectra of cyanamide and cyanamide-d2 by rotation—inversion theory

Rotation—inversion theory (RINV) is applied for analysis of microwave and infrared spectroscopic data of cyanamide-d_o and -d₂. It is found that for the light species the whole set of known data may be reproduced by one set of RINV kinetic parameters, a potential barrier of V(0) ≈450 cm^?1 and an equilibrium value of 45.5° for the inversion angle. The known spectral data of the d₂ species cannot be explained by the RINV approach to a satisfactory degree. Inclusion of structure relaxation for either the DND angle or the ND bond length or both was fould not to reduce the inadequacy of the RINV model.     

Numerical analysis of the rotational relaxation time of spectrin segments and spectrin heterodimer in dilute aqueous solution

The rotational relaxation time for different models of the spectrin αβ-heterodimer and spectrin subunits were obtained through numerical simulation making use of the so-called rigid-body approximation. Based on information on the helix structure of the 106 aminoacids in the repeating motif of spectrin, three different models with varying degree of refinement were set up to represent the spectrin subunits: the two-bead, the many-bead and the shell model. For one- and two-subunit spectrin the relaxation time was found to be 20 ± 4 ns and 92 ± 5 ns, respectively. The last result conforms well with available experimental data from transient electric birefringence measurements. For the αβ-heterodimer two different models were applied: a chain of beads (pearl necklace model) and a more refined so-called San necklace model. Using the San necklace model, the relaxation time was found to be in the range of 9 to 18 μs (depending on the flexibility of the joint), which is in accordance with what has been obtained from intrinsic viscosity measurements, but considerably higher than experimental data from measurements of transient electric birefringence.     

Intermolecular relaxation in glycerol as revealed by field cycling 1H NMR relaxometry dilution experiments

(1)H spin-lattice relaxation rates R(1) = 1/T(1) have been measured for partly deuterated glycerol-h(5) diluted in fully deuterated glycerol-h(0) for progressively lower concentrations of glycerol-h(5). By means of the field cycling (FC) technique relaxation dispersion data, R(1)(ω), have been collected for several temperatures in the frequency range of 10 kHz-20 MHz. In order to disclose the spectral shape of the intra- and intermolecular relaxation, extrapolation of the relaxation data to the zero concentration limit has been performed. The paper confirms that the low frequency excess contribution to the total relaxation rate R(1)(ω) previously reported for several liquids is of intermolecular origin and reflects translational motion, whereas the high-frequency part is attributed to molecular rotation. Thus, intra- and intermolecular relaxation contributions are spectrally separated. The intermolecular relaxation itself contains also a contribution from rotational motion, which is due to non-central positions of the interacting nuclei in the molecule. This eccentricity effect is quantitatively reproduced by treating the intermolecular spectral density as a sum of translational-like (described by the free diffusion model) and rotational-like contributions (described by a Cole-Davidson function). Applying frequency-temperature superposition master curves as well as individual relaxation dispersion data, R(1)(ω), are analyzed. It is demonstrated that, in spite of the rotational influence, the translational diffusion coefficients, D(T), can be extracted from the (1)H relaxation dispersion which gives (1)H NMR relaxometry the potential to become a routine technique determining the diffusion coefficient in liquids.     

分数Maxwell模型应用于PTFE松弛模量的研究

用分数Maxwell模型对聚合物PTFE(Polytetrafluoethylene)的应力松弛过程进行了研究. 分数Maxwell模型的渐近行为是确定其参数的基本依据, 但根据实验数据确定的松弛时间与渐近解成立的条件并不自恰. 通过适当选定松弛时间, 利用起始时段的实验数据确定初始松弛指数和松弛模量, 并适当优化末端松弛指数, 分数Maxwell模型可以对粘弹性应力松弛过程给出非常好的描述.     

Wide-frequency-range dielectric response of polystyrene latex dispersions

In this work we analyze the dielectric properties of dilute colloidal suspensions of nonconducting spherical particles with a thin electrical double layer from experimental data obtained by performing impedance spectroscopy experiments over a broad frequency range, from 20 Hz to 1 GHz. The electrode polarization correction was made by fitting a circuit model in the complex impedance plane (impedance spectrum) using a constant phase angle (CPA) element to fit the electrode polarization in series with the sample impedance. This simple procedure is found to be effective in eliminating the electrode contribution. The dielectric response shows two different dispersions, the alpha relaxation (counterion relaxation) that occurs at low kilohertz frequencies, and the delta relaxation (Maxwell-Wagner effect) found in the MHz range. These are reasonably well fitted over a broad frequency range by the theoretical expressions given by a simplified standard model (not including anomalous conduction) and a generalized model (including anomalous conduction) for the low-frequency dispersion, plus Maxwell-Wagner-O'Konski theory for the delta relaxation in the mid-frequency range. An analysis was also made of the need to include, for these latices, the effects of ion mobility in the Stern layer in order for the values of the zeta-potential obtained from electrophoretic and dielectric data to be compatible with each other.     

Structural relaxation of amorphous Ge38S62 studied by length dilatometry and calorimetry

The structural relaxation of Ge₃₈S₆₂ glass has been studied by length dilatometry and calorimetry. The Tool-Narayanaswamy-Moynihan model was applied on obtained data of structural relaxation and parameters of this model were determined: Δh*= 483±2 kJ mol^-1, ln(A/s)= -81±1, β= 0.7±0.1 and x=0.6±0.1. Both dilatometric and calorimetric relaxation data were compared on the basis of the fictive relaxation rate. It was found that the relaxation rates are very similar and well correspond to the prediction of phenomenological model. This revised version was published online in July 2006 with corrections to the Cover Date.     

Structural relaxation in complex liquids: non-Markovian dynamics in a bistable potential

The time correlation function C(t) identical with of the distance fluctuations of a particle moving in a bistable potential under the action of fractional Gaussian noise (fGn) is calculated from a Smoluchowski-type equation derived from a generalized Langevin equation (GLE). The time derivative of this function, dC(t)dt, is compared with data from optical Kerr effect measurements of liquid crystal dynamics in the vicinity of the isotropic-to-nematic transition, which are related to the time derivative of an orientational correlation function. A number of characteristic features of the experimental decay curves, including short and intermediate time power law behavior and long time exponential relaxation, are qualitatively reproduced by the analytical calculations, even though the latter do not explicitly treat orientational degrees of freedom. The GLE formalism with fGn was, in fact, originally proposed as a model of protein conformational fluctuations, so the present results suggest that it may also serve more generally as a model of structural relaxation in complex condensed phase media.     

The bending recovery of polymer films. I. A phenomenological model

When a flat film is bent to some fixed curvature, held at this state for some time, and then released, its curvature is usually observed to drop instantaneously to some finite value and then gradually decrease with time. This phenomenon, generally referred to as bending recovery, has been modeled by simple extension of the classical plate-bending theory to linear-viscoelastic materials. The model assumes that the relaxation spectra in tension and compression are dissimilar but are interrelated through a simple temporal shift. Experimental data, including instantaneous recovery at ambient and elevated temperatures as well as recovery over extended times, have been generated for four films with widely different relaxation characteristics. The data are in reasonable agreement with predictions of the model if a constant value of the compressive shift parameter (see text) is used for all materials. The model indicates that the bending recovery of a polymer film is intimately related to its relaxation spectrum and can be effectively manipulated by changes in temperature and winding time.