We analyzed the complex dielectric and Raman spectra of hydrogen-bond liquids in the microwave to terahertz frequency range. As for water and methanol, the high-frequency component of the dielectric spectrum, i.e., the small deviation from the principal Debye relaxation, clearly corresponds to the Raman spectrum. This indicates that the cooperative relaxation, accompanied by huge polarization fluctuation, is virtually not Raman active, whereas the faster processes reflect common microscopic dynamics. For ethylene glycol, the shape of the Raman spectrum also resembles that of the high-frequency deviation of the dielectric spectrum, but, additionally, a weak manifestation of the cooperative relaxation arising from quadrupolar conformers is detected.

The cluster structures observed by means of mass spectrometry for binary mixturesstert-butyl alcohol (TBA)-H 2 O and tetrahydrofuran (THF)-D 2 Oswith varying mixing ratios exhibit striking contrast, even though both TBA and THF are miscible with water at any mixing ratio. In the TBA-H 2 O mixtures at TBA mole fractions of (X TBA ) e 0.01-0.025, some of the H 2 O molecules in the H 2 O clusters are replaced by TBA molecules. For 0.01-0.025 e X TBA e 0.2-0.3, the self-aggregation of TBA forms dominant cluster structures, and the hydrogen-bonded water clusters are disintegrated with increasing X TBA . This TBA self-aggregation is reduced with further increasing TBA at X TBA g 0.3. However, in the THF-D 2 O mixtures, THF molecules have a weak additional interaction with D 2 O clusters, and the self-aggregation of THF is not promoted in the THF-D 2 O mixtures. The D 2 O clusters still exist, even at a THF mole fraction of X THF ) 0.3. On the basis of the observed cluster structure, the mechanism for the mixing between water and the organic solvent and the controlling factors in the self-aggregation are proposed.

We highlight versatile applicability of a structure-factor indirect Fourier transformation (IFT) technique, hereafter called SQ-IFT. The original IFT aims at the pair distance distribution function, p(r), of colloidal particles from small angle scattering of X-rays (SAXS) and neutrons (SANS), allowing the conversion of the experimental form factor, P(q), into a more intuitive real-space spatial autocorrelation function. Instead, SQ-IFT is an interaction potential model-free approach to the 'effective' or 'experimental' structure factor to yield the pair correlation functions (PCFs), g(r), of colloidal dispersions like globular protein solutions for small-angle scattering data as well as the radial distribution functions (RDFs) of molecular liquids in liquid diffraction (LD) experiments. We show that SQ-IFT yields accurate RDFs of liquid H(2)O and monohydric alcohol reflecting their local intermolecular structures, in which q-weighted structure function, qH(q), conventionally utilized in many LD studies out of necessity of performing direct Fourier transformation, is no longer required. We also show that SQ-IFT applied to theoretically calculated structure factors for uncharged and charged colloidal dispersions almost perfectly reproduces g(r) obtained as a solution of the Ornstein-Zernike (OZ) equation. We further demonstrate the relevance of SQ-IFT in its practical applications, using SANS effective structure factors of lysozyme solutions reported in recent literatures which revealed the equilibrium cluster formation due to coexisting long range electrostatic repulsion and short range attraction between the proteins. Finally, we present SAXS experiments on human serum albumin (HSA) at different ionic strength and protein concentration, in which we discuss the real space picture of spatial distributions of the proteins via the interaction potential model-free route.

Low-frequency Raman scattering spectra have been measured for tert-butyl alcohol ͑TBA͒-water and tetrahydrofuran ͑THF͒-water binary mixtures as a function of concentration. We confirmed the isosbestic point in the reduced Raman spectra Љ() of the TBA-water and THF-water mixtures. The Љ() spectra could be decomposed into a linear combination of the neat TBA spectrum and the pure water spectrum in the frequency range from 80 to 400 cm Ϫ1 . On the other hand, below 80 cm Ϫ1 , the Љ() spectra could not be decomposed into a linear combination. The superposed spectra deviated systematically from the experimental spectra as a function of solute concentration. This result indicated that cooperative dynamics was present in TBA-water and THF-water mixtures although the intermolecular vibrations showed independent character.

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Using small-angle X-ray scattering (SAXS), we have studied the initial stage (nucleation and oligomerization) of actin polymerization induced by raising temperature in a stepwise manner from 1°C to 30°C at low ionic strength (4.0 mg ml−1 actin in G-buffer). The SAXS experiments were started from the mono-disperse G-actin state, which was confirmed by comparing the scattering pattern in q- and real space with X-ray crystallographic data. We observed that the forward scattering intensity I(q → 0), used as an indicator for the extent of poly-merization, began to increase at ∼14°C for Mg-actin and ∼20°C for Ca-actin, and this critical temperature did not depend on the nucleotide species, i.e., ATP or ADP. At the temperatures higher than ∼20°C for Mg-actin and ∼25°C for Ca-actin, the coherent reflection peak, which is attributed to the helical structure of F-actin, appeared. The pair-distance distribution functions, p(r), corresponding to the frequency of vector lengths (r) within the molecule, were obtained by the indirect Fourier transformation (IFT) of the scattering curves, I(q). Next, the size distributions of oligomers at each temperature were analyzed by fitting the experimentally obtained p(r) with the theoretical p(r) for the helical and linear oligomers (2–13mers) calculated based on the X-ray crystallographic data. We found that p(r) at the initial stage of polymerization was well accounted for by the superposition of monomer, linear/helical dimers, and helical trimer, being independent of the type of divalent cations and nucleotides. These results suggest that the polymerization of actin in G-buffer induced by an increase in temperature proceeds via the elongation of the helical trimer, which supports, in a structurally resolved manner, a widely believed hypothesis that the polymerization nucleus is a helical trimer.

Optical molecular sensing techniques are often limited by the refractive index change associated with the probed interactions. In this work, we present a closed form analytical model to estimate the magnitude of optical refractive index change arising from protein-protein interactions. The model, based on the Maxwell Garnett effective medium theory and first order chemical kinetics serves as a general framework for estimating the detection limits of optical sensing of molecular interactions. The model is applicable to situations where one interacting species is immobilized to a surface, as commonly done, or to emerging techniques such as Back-Scattering Interferometry (BSI) where both interacting species are un-tethered. Our findings from this model point to the strong role of as yet unidentified factors in the origin of the BSI signal resulting in significant deviation from linear optical response.