The three-dimensional structure of water confined in nanoporous vycor glass

Neutron diffraction data, in conjunction with isotopic substitution of deuterium (D) for hydrogen (H), have been analyzed to determine the three-dimensional structure of water confined in vycor, an archetypal hydrophilic porous silica glass containing channels or pores of approximately 40 A diameter. The data have been incorporated into a Monte Carlo computer simulation of the confined water system, and the site-site potentials have been iteratively refined in order to produce a model ensemble which is consistent with both the neutron diffraction data and two possible geometries of the vycor pores (cylindrical and spherical). This approach has allowed us to investigate in detail the contributions to the experimentally accessible partial pair correlation functions, and ascertain whether particular features arise from interactions of the water molecules with the substrate surface, or from purely geometrical confinement effects. We observe a significant decrease in the first shell water oxygen-oxygen co-ordination number, and a decrease in the number of hydrogen bonds per water molecule from approximately 3.6 in bulk water to approximately 2.2 in confinement. In addition, we observe a significant shift inward of the second peak in the water oxygen-water oxygen coordination shell. Overall, we therefore find that the structure of the water in vycor is strongly perturbed relative to the bulk.     

Microscopic model of true strain softening and hardening in a polymer glass

A simple microscopic model is proposed to describe the true strain softening and hardening behavior of a polymer glass. Equations of motion for the polymer chain embedded in a polymer matrix have been derived and investigated both analytically and numerically. The model correctly predicts both true strain softening and hardening phenomena. The model also allows a new interpretation of the microscopic origin of true strain softening in a polymer glass.     

Protein structure optimization using improved simulated annealing algorithm on a three-dimensional AB off-lattice model

This paper proposed an improved simulated annealing (ISA) algorithm for protein structure optimization based on a three-dimensional AB off-lattice model. In the algorithm, we provided a general formula used for producing initial solution, and designed a multivariable disturbance term, relating to the parameters of simulated annealing and a tuned constant, to generate neighborhood solution. To avoid missing optimal solution, storage operation was performed in searching process. We applied the algorithm to test artificial protein sequences from literature and constructed a benchmark dataset consisting of 10 real protein sequences from the Protein Data Bank (PDB). Otherwise, we generated C_α space-filling model to represent protein folding conformation. The results indicate our algorithm outperforms the five methods before in searching lower energies of artificial protein sequences. In the testing on real proteins, our method can achieve the energy conformations with C_α-RMSD less than 3.0 Å from the PDB structures. Moreover, C_α space-filling model may simulate dynamic change of protein folding conformation at atomic level.     

Local structure of a phase-separating binary mixture in a mesoporous glass matrix studied by small-angle neutron scattering

The mesoscopic structure of the binary system isobutyric acid + heavy water (D(2)O) confined in a porous glass (controlled-pore silica glass, mean pore width ca. 10 nm) was studied by small-angle neutron scattering at off-critical compositions in a temperature range above and below the upper critical solution point. The scattering data were analyzed in terms of a structure factor model similar to that proposed by Formisano and Teixeira [Eur. Phys. J. E 1, 1 (2000)], but allowing for both Ornstein-Zernike-type composition fluctuations and domainlike structures in the microphase-separated state of the pore liquid. The results indicate that the phase separation in the pores is shifted by ca. 10 K and spread out in temperature. Microphase separation is pictured as a transition from partial segregation at high temperature, due to the strong preferential adsorption of water at the pore wall, to a tube or capsule configuration of the two phases at low temperatures, depending on the overall composition of the pore liquid. Results for samples in which the composition of the pore liquid can vary with temperature due to equilibration with extra-pore liquid are consistent with this picture.     

Inertial suppression of protein dynamics in a binary glycerol-trehalose glass

The traditional approach used to predict the ability of a glassy matrix to maximally preserve the activity of a protein solute is the glass transition temperature (T(g)) of the glass. Recently it has been shown that the addition of a low T(g) diluent (glycerol) can rigidify the structure of a high T(g) glassy matrix in binary glycerol-trehalose glasses. The optimal density of glycerol in trehalose minimizes the average mean square displacements of non-exchangeable protons in the glass samples. The amount of glycerol added to a trehalose glass coincides with the maximal recovery of biological activity in a separate study using similar binary glass samples. In this study, we use molecular dynamics (MD) simulations to investigate the dynamics of a hydrated protein encased in glycerol, unary trehalose and binary glycerol-trehalose glasses. We have found that we are able to reproduce the rigidification of the glycerol-trehalose glassy matrix and that there is a direct correlation between bulk glass dynamics and the extent of atomic fluctuation of protein atoms. The detailed microscopic picture that emerges is that protein dynamics are suppressed mainly by inertia of the bulk glass and to a lesser extent specific interactions at the protein-solvent interface. Thus, the inertia of the glassy matrix may be an influential factor in the determination of pharmaceutically relevant formulations.     

Fish-Bite structure by three-dimensional hydrogen-bond acceptor: IR spectroscopy of pyrrole and N-methylpyrrole binary clusters

The N-H[ellipsis (horizontal)]π hydrogen-bonded (H-bonded) structures of pyrrole (Py) and N-methylpyrrole (NMPy) binary clusters have been studied by IR cavity ringdown spectroscopy and density functional theory calculations. The Py(1)-NMPy(1) cluster has an "L-shape" structure, which is formed by an ordinary H-bond between a N-H donor of Py and a π-electron cloud acceptor of NMPy. The Py(2)-NMPy(1) cluster has a "Cyclic" structure, which is also formed by ordinary N-H[ellipsis (horizontal)]π H-bonds as well as the weak C-H[ellipsis (horizontal)]π H-bond between the methyl CH group and the π cloud acceptor of Py. On the other hand, the Py(1)-NMPy(2) cluster shows an extraordinary structure, in which the single donor NH group is surrounded by a three-dimensional H-bond acceptor formed by two aromatic π electron clouds. We call the Py(1)-NMPy(2) cluster as the "Fish-Bite" structure. The Py(1)-NMPy(2) cluster exhibits a redshifted NH stretch by 157 cm(-1) from the Py monomer, which is larger than 94 cm(-1) of the Py(1)-NMPy(1) cluster. However, both Py(1)-NMPy(1) and Py(1)-NMPy(2) clusters have calculated IR intensities of 169 and 163 km∕mol, respectively. This result indicates that not only the N-H[ellipsis (horizontal)]π H-bonds but also the dipole-dipole interaction between Py and NMPy contributes to the Fish-Bite Py(1)-NMPy(2) cluster formation.     

A study of the static yield stress in a binary Lennard-Jones glass

The stress-strain relations and the yield behavior of a model glass (a 80:20 binary Lennard-Jones mixture) is studied by means of molecular dynamics simulations. In a previous paper it was shown that, at temperatures below the glass transition temperature, Tg, the model exhibits shear banding under imposed shear. It was also suggested that this behavior is closely related to the existence of a (static) yield stress (under applied stress, the system does not flow until the stress sigma exceeds a threshold value sigmay). A thorough analysis of the static yield stress is presented via simulations under imposed stress. Furthermore, using steady shear simulations, the effect of physical aging, shear rate and temperature on the stress-strain relation is investigated. In particular, we find that the stress at the yield point (the "peak"-value of the stress-strain curve) exhibits a logarithmic dependence both on the imposed shear rate and on the "age" of the system in qualitative agreement with experiments on amorphous polymers, and on metallic glasses. In addition to the very observation of the yield stress which is an important feature seen in experiments on complex systems like pastes, dense colloidal suspensions and foams, further links between our model and soft glassy materials are found. An example is the existence of hysteresis loops in the system response to a varying imposed stress. Finally, we measure the static yield stress for our model and study its dependence on temperature. We find that for temperatures far below the mode coupling critical temperature of the model (Tc = 0.435 in Lennard-Jones units), sigmay decreases slowly upon heating followed by a stronger decrease as Tc is approached. We discuss the reliability of results on the static yield stress and give a criterion for its validity in terms of the time scales relevant to the problem.     

Single particle jumps in a binary Lennard-Jones system below the glass transition

We study a binary Lennard-Jones system below the glass transition with molecular dynamics simulations. To investigate the dynamics we focus on events (jumps) where a particle escapes the cage formed by its neighbors. Using single particle trajectories we define a jump by comparing for each particle its fluctuations with its changes in average position. We find two kinds of jumps: "reversible jumps," where a particle jumps back and forth between two or more average positions, and "irreversible jumps," where a particle does not return to any of its former average positions, i.e., successfully escapes its cage. For all investigated temperatures both kinds of particles jump and both irreversible and reversible jumps occur. With increasing temperature, relaxation is enhanced by an increasing number of jumps and growing jump lengths in position and potential energy. However, the waiting time between two successive jumps is independent of temperature. This temperature independence might be due to aging, which is present in our system. We therefore also present a comparison of simulation data with three different histories. The ratio of irreversible to reversible jumps is also increasing with increasing temperature, which we interpret as a consequence of the increased likelihood of changes in the cages, i.e., a blocking of the "entrance" back into the previous cage. In accordance with this interpretation, the fluctuations both in position and energy are increasing with increasing temperature. A comparison of the fluctuations of jumping particles and nonjumping particles indicates that jumping particles are more mobile even when not jumping. The jumps in energy normalized by their fluctuations are decreasing with increasing temperature, which is consistent with relaxation being increasingly driven by thermal fluctuations. In accordance with subdiffusive behavior are the distributions of waiting times and jump lengths in position.     

Probing electronic environment in gamma irradiated sodium borosilicate glass and simulated waste glass: a perturbed angular correlation spectroscopy study

Journal of Radioanalytical and Nuclear Chemistry - Time Differential Perturbed Angular Correlation (TDPAC) has been used to investigate the local structural changes (if any) in Sodium borosilicate...     

Corrosion performances of a Nickel-free Fe-based bulk metallic glass in simulated body fluids

The corrosion performance of a Nickel-free Fe-based bulk metallic glass (BMG), Fe₄₁Co₇Cr₁₅Mo₁₄C₁₅B₆Y₂ alloy, in Hank’s solution with pH value 7.4 and artificial saliva solution with pH value 6.3, was investigated by electrochemical techniques, aiming to assess the feasibility of Fe-based BMG as potential biomaterial. It was found that Fe₄₁Co₇Cr₁₅Mo₁₄C₁₅B₆Y₂ BMG shows superior corrosion resistance in both simulated body fluids (SBF). The EIS analysis and cyclic polarization measurements indicated that the Fe₄₁Co₇Cr₁₅Mo₁₄C₁₅B₆Y₂ BMG has larger polarization resistance value than that of 316L SS. The pitting corrosion potentials of Fe₄₁Co₇Cr₁₅Mo₁₄C₁₅B₆Y₂ BMG are much higher than that of the 316L SS, resulting in very few ions releasing into the SBFs while a significant amount of Ni and Fe ions release was found for 316L SS under the same condition.     

Nonresonant dielectric hole burning in neat and binary organic glass formers

Binary mixtures of the molecular glass former 2-picoline in oligostyrene, in which the dielectric response of 2-picoline exhibits a particularly broad distribution of correlation times, are investigated by nonresonant dielectric hole-burning (NDHB) spectroscopy and the results are compared with NDHB in neat systems, in particular, glycerol. It turns out that in both substance classes spectral selectivity is achieved, which indicates that dynamics is heterogeneous, i.e., slow and fast responses coexist in the material. However, in binary systems the position of the spectral modifications is completely determined by the spectral density of the pump field, and thus shifts linearly with burn frequency as expected, also at pump frequencies around the alpha-relaxation maximum. It is shown that in binary systems the lifetime tau(rec) of the spectral modifications is determined by the burn frequency omega(p) and exceeds its inverse by about one order of magnitude, indicating long-lived dynamic heterogeneity. The data are described in terms of a previously suggested model of dynamically selective heating, which was extended to include intrinsic nonexponential relaxation. It turns out that the spectral broadening in binary mixtures is not only due to pronounced dynamic heterogeneity, but partially also due to intrinsic broadening of the relaxation function.     

Structural relaxation and glass transition behavior of binary hard-ellipse mixtures

Structural relaxation and glass transition in binary hard-spherical particle mixtures have been reported to exhibit unusual features depending on the size disparity and composition. However, the mechanism by which the mixing effects lead to these features and whether these features are universal for particles with anisotropic geometries remains unclear. Here, we employ event-driven molecular dynamics simulation to investigate the dynamical and structural properties of binary two-dimensional hard-ellipse mixtures. We find that the relaxation dynamics for translational degrees of freedom exhibit equivalent trends as those observed in binary hard-spherical mixtures. However, the glass transition densities for translational and rotational degrees of freedom present different dependencies on size disparity and composition. Furthermore, we propose a mechanism based on structural properties that explain the observed mixing effects and decoupling behavior between translational and rotational motions in binary hard-ellipse systems.     

Crystal structure of a continuous three-dimensional DNA lattice

DNA has proved to be a versatile material for the rational design and assembly of nanometer scale objects. Here we report the crystal structure of a continuous three-dimensional DNA lattice formed by the self-assembly of a DNA 13-mer. The structure consists of stacked layers of parallel helices with adjacent layers linked through parallel-stranded base pairing. The hexagonal lattice geometry contains solvent channels that appear large enough to allow 3'-linked guest molecules into the crystal. We have successfully used these parallel base pairs to design and produce crystals with greatly enlarged solvent channels. This lattice may have applications as a molecular scaffold for structure determination of guest molecules, as a molecular sieve, or in the assembly of molecular electronics. Predictable non-Watson-Crick base pairs, like those described here, may present a new tool in structural DNA nanotechnology.     

新型三维微孔砷酸铟InAsO4(H2O)2的合成及结构

首次以有机胺为结构导向剂,在水热条件下合成了微孔砷酸铟材料InAsO4-1,并对其进行了结构及性质表征。X射线单晶结构解析表明InAsO4-1分子式为InAsO4(H2O)2。晶体学数据为：Pbca,a=0.9090(4)nm,b=1.0344(4)nm,c=1.0468(4)nm,α=β=Υ=90°,V=0.9843(7)nm^3,Z=8,R=0.0480,Rw=0.1045。InAsO4-1具有三维结构,其a,b方向分别有4元环及6元环的一维孔道,结构中还含有一8^16^44^2笼,热重分析显示其结构水较稳定。     

Shear banding structure in viscoelastic micellar solutions

 Theoretically, it has been shown that worm-like micellar solutions of surfactant can, for a shear rate γ˙ greater than a critical value γ˙_c, undergo a transition giving a plateau evolution (σ=σ_c) of the shear stress σ against shear rate γ˙. We report here on a experimental study of the linear and nonlinear rheological behaviour of aqueous CTAB solutions with NaNO₃ as added salt. With this system, it is possible to observe the evolution of the fundamental characteristics of the flow curve, i.e., the shear rate γ˙_1c at which a shear banding structure appears and the second critical shear rate γ˙_2c characterizing the end of the shear stress plateau followed by a new increased shear stress. For the first time, experimentally, we obtained evidence for the existence and the evolution of γ˙_2c against CTAB and salt concentrations and temperature variations. Experimental results are compared to theoretical predictions correlating σ_c, γ˙_1c and G ₀ (the shear modulus) for Maxwellian micellar solutions. Received: 4 July 1996 Accepted: 19 November 1996     

Thermal study of glass transitions in binary systems of simple hydrocarbons

Glass transition phenomena of four binary systems composed of simple hydrocarbons were studied by means of the differential thermal analysis (DTA). For all the systems, a definite glass transition was observed and a monotonous relation between the glass transition temperature (T _g) and composition (x) was obtained. The composition dependence ofT _g was analyzed in terms of the entropy theory based on the regular solution model. The theoretical prediction could not reproduce our results other than (1-butene)_x(1-pentene)_1?x system. This disagreement is considered to be due to deviations of the present systems from the regular solution, and the accompanying excess configurational entropy S_c ^E was estimated as a function of composition. Extraordinarily large values of S _c ^E ? were obtained for (propene)_x(propane)_1?x and (propene)inx(1-pentene)_1?x systems.     

Spectra and structure of binary azeotropes VI-benzene-methanol

Benzene and methanol make a minimum boiling point homogeneous binary azeotrope with the mole ratio 2:3. Some characteristic vibrational modes, as well as ¹H NMR signals change due to the azeotrope formation. The extend of interaction of these molecules causes significant changes on some vibrational modes involved, and ¹H NMR signals show some changes on their position. No IR, Raman, and NMR spectra have been reported for this constant boiling mixture, also there has not been any attempt to investigate the unit-structure of this azeotrope. In this work the FTIR, FT-Raman, and ¹H NMR spectra of pure benzene, pure methanol, and corresponding azeotrope were recorded, mutual influences resulting from azeotrope formation have been analyzed, and spectral changes has been discussed. The unit-structure of cluster has been deduced based on mole ratio, boiling point depression of constituents, and comparison among the spectra obtained by FTIR, FT-Raman, and ¹H NMR techniques.     

Spectra and structure of binary azeotropes V-acetone-cyclopentane

Acetone and cyclopentane make a minimum boiling homogeneous binary azeotrope with mole ratio 2:3. Some characteristic vibrational modes, as well as (1)H NMR signals change due to the azeotrope formation. The extend of interaction of these molecules causes significant changes on some vibrational modes involved and (1)H NMR signals show some changes on their position. In this work the FTIR and (1)H NMR spectra of pure acetone, pure cyclopentane and corresponding azeotrope were recorded, mutual influences resulting from azeotrope formation have been analyzed, and spectral changes has been discussed. The unit-structure of cluster have been deduced, based on mole ratio, boiling point depression of constituents, and comparison between the spectra obtained by FTIR and (1)H NMR techniques.