On self-interacting oligoribonucleotides. I. Absorption and optical rotatory dispersion of 2′-5′- and 3′-5′-oligoguanylic acids

A series of 2′-5′-oligoguanylic acids are prepared by reacting G(cyclic)p with takadiastase T1 ribonuclease and separating the products chromatographically. The 3′-5′-oligoguanylic acids are obtained by separating the products of alkaline degradation of 3′-5′-poly(G). The optical rotatory dispersion and hypochromism of both 2′-5′- and 3′-5′-oligoguanylic acids are studied at two different pH. The optical rotatory dispersion spectrum of 2′-5′-GpG is significantly different from that of 3′-5′-GpG. The magnitude of rotation of the long-wavelength peak of 2′-5′-GpG is larger than that of 3′-5′-GpG. This finding contradicts the explanation that the extra stability and more intense circular dichroism band of other 3′-5′-dinucleoside monophosphates is due to H-bond formation between 2′-OH and either the base or the phosphate oxygen. The end phosphate group has a marked effect on the spectrum of GpG between 230 and 250 mμ. In addition the optical rotatory dispersion spectra of 2′-5′ exhibit strong pH, temperature, and solvent dependence between 230 and 250 mμ. ΔH and AS for order ⇌ disorder transition is estimated to be 9.7 kcal/mole and 35.2 eu, respectively. The optical rotatory dispersion spectra of guanine-rich oligoribonucleotides, GpGpC, GpGpU, GpGpGpC, and GpGpGpU are compared to the calculated optical rotatory dispersion from the semiempirical expression of Cantor and Tinoco, using measured optical rotatory dispersion of dimers. Contrary to previous studies, agreement is found not at all satisfactory. However, optical rotatory dispersion of 3′-5′-GpGpGpC and GpGpGpU can be estimated from the semiempirical expression, if a next-nearest interaction parameter is introduced empirically. Such interaction parameter can be calculated from the measured properties of trinucleotide sequences like GpGpG, GpGpC, and GpGpU, assuming that only the nearest-neighbor interaction is important. The optical rotatory dispersion of single-stranded poly(G) is also predicted. The importance of syn-anti equilibrium and next-nearest-neighbor interaction in oligoguanylic acids is suggested as a probable explanation.

Studies on the brookite-rutile transformation

Brookite, the orthorhombic modification of titanium dioxide, transforms to the tetragonal modification, rutile, on heating. The kinetics and energetics of the transformation have been studied. Below 715±10°C, the rate of transformation is extremely slow. There appears to be little or no induction time. The kinetic data can be fitted reasonably well by the first-order equation. The energy of activation is about 60 kcal/mole and the frequency factor is of the order of 1013 h-1. The entropy of activation from Eyring's theory is about -18 cal/mole deg. at 800°C. The heat of this transformation is -100±75 cal/mole. The kinetic results may be explained qualitatively in terms of various analogies but more clearly by the application of the order-disorder theory to diffusionless transformation in solids. It has been shown that the ratio of propagation rate constant to the nucleation rate constant is small and that there is little or negligible phase aggregation.

Freezing of a colloidal liquid subject to shear flow

A nonequilibrium generalization of the density-functional theory of freezing is proposed to investigate the shear-induced first-order phase transition in colloidal suspensions. It is assumed that the main effect of a steady shear is to break the symmetry of the structure factor of the liquid and that for small shear rate, the phenomenon of a shear-induced order-disorder transition may be viewed as an equilibrium phase transition. The theory predicts that the effective density at which freezing takes place increases with shear rate. The solid (which is assumed to be a bcc lattice) formed upon freezing is distorted and specifically there is less order in one plane compared with the order in the other two perpendicular planes. It is shown that there exists a critical shear rate above which the colloidal liquid does not undergo a transition to an ordered (or partially ordered) state no matter how large the density is. Conversely, above the critical shear rate an initially formed bcc solid always melts into an amorphous or liquidlike state. Several of these predictions are in qualitative agreement with the light-scattering experiments of Ackerson and Clark. The limitations as well as possible extensions of the theory are also discussed.

Spectroscopic investigations of phase transitions in complex solids

Spectroscopic methods have provided information of seminal importance in understanding phase transitions in solids. After briefly examining some fundamental concept related to phase transitions, we shall discuss several case studies particularly involving the use of vibrational (IR and Raman) spectroscopy. Examples will include both order-disorder and displacive transitions. Under the former are included transitions in nitrates, ammonium halides, alkylammonium salts, plastic state of C60 and superionic conductors (specially CsHSO4). In addition, we shall discuss some aspects of incommensurate phase transitions, the glass transition and electronic phase transitions. Transitions of phosphonitrilic halide tetramers and alkane dicarboxylic acids are also examined

Molecular-dynamics studies of systems of confined dumbbell molecules

We present the results of molecular-dynamics simulations of systems of dumbbell molecules confined by parallel molecular walls. We have carried out systematic studies of three cases: freezing, steady flows, and stick-slip friction. We find that the molecular orientational degrees of freedom cause the surface layers to deviate from a planar configuration. Nevertheless, steady flows, in a channel as narrow as 15 molecular sizes, display continuum behavior. A range of mechanisms in the dynamics of the freezing of a confined fluid is found, as a function of the wall-fluid interactions and the bond length of the dumbbell molecules. The simple order-disorder transition associated with stick-slip motion in the presence of a layer of monoatomic lubricant molecules is supplanted by more complex behavior due to rotational degrees of freedom of the diatomic molecules.

On the formation of poly(ethyleneoxide)-poly(vinylalcohol) blends

Poly(ethyleneoxide)-poly(vinylalcohol) blends were prepared and characterized using thermal, spectroscopic and structural methods, By all indications the blends appear to be microscopically inhomogeneous with no strong interpolymer bonding. The high degree of crystallinity in PEO regions induces a significant degree of ordering in neighbouring PVA regions, as evident from thermal properties. PVA obtained from solvent evaporation exhibits an irreversible endothermic transition which could be order-disorder type. Both IR and NMR spectroscopies also suggest the presence of subtle structural ordering influence of PEO on PVA. It is found to be possible to prepare self supporting films of the blends which consists of fine dispersion of PEO and PVA in each other. (C) 1999 Elsevier Science Ltd. All rights reserved.

Thermodynamic studies on NdFeO3(s)

The enthalpy increments and the standard molar Gibbs energy of formation of NdFeO3(s) have been measured using a hightemperature Calvet microcalorimeter and a solid oxide galvanic cell, respectively. A lambda-type transition, related to magnetic order-disorder transformation (antiferromagnetic to paramagnetic), is apparent from the heat capacity data at similar to 687 K. Enthalpy increments, except in the vicinity of transition, can be represented by a polynomial expression: {Hdegrees(m)(T)-Hdegrees(m) (298.15 K)} /J(.)mol(-1) (+/- 0.7%)=-53625.6+146.0(T/K) +1.150 X 10(-4)(T/K)(2) +3.007 x 10(6)(T/K)(-1); (298.15 less than or equal to T/K less than or equal to 1000). The heat capacity, the first differential of {Hdegrees(m)(T)-Hdegrees(m)(298.15 K)}with respect to temperature, is given by Cdegrees(pm)/J(.)K(-1.)mol(-1)=146.0+ 2.30x10(-4) (T/K) - 3.007 X 10(6)(T/K)(-2). The reversible emf's of the cell, (-) Pt/{NdFeO3(s) +Nd2O3(s)+Fe(s)}//YDT/CSZ// Fe(s)+'FeO'(s)}/Pt(+), were measured in the temperature range from 1004 to 1208 K. It can be represented within experimental error by a linear equation: E/V=(0.1418 +/- 0.0003)-(3.890 +/- 0.023) x 10(-5)(T/K). The Gibbs energy of formation of solid NdFeO, calculated by the least-squares regression analysis of the data obtained in the present study, and data for Fe0.95O and Nd2O3 from the literature, is given by Delta(f)Gdegrees(m)(NdFeO3 s)/kJ (.) mol(-1)( +/- 2.0)=1345.9+0.2542(T/K); (1000 less than or equal to T/K less than or equal to 1650). The error in Delta(f)Gdegrees(m)(NdFeO3, s, T) includes the standard deviation in emf and the uncertainty in the data taken from the literature. Values of Delta(f)Hdegrees(m)(NdFeO3, s, 298.15 K) and Sdegrees(m) (NdFeO3 s, 298.15 K) calculated by the second law method are - 1362.5 (+/-6) kJ (.) mol(-1) and 123.9 (+/-2.5) J (.) K-1 (.) mol(-1), respectively. Based on the thermodynamic information, an oxygen potential diagram for the system Nd-Fe-O was developed at 1350 K. (C) 2002 Elsevier Science (USA).

Thermodynamic properties of SmFeO3(S) and SM3R5O12(S)

The enthalpy increments and the standard molar Gibbs energy (G) of formation of SmFeO3(S) and SM3Fe5O12(s) have been measured using a Calvet micro-calorimeter and a solid oxide galvanic cell, respectively. A X-type transition, related to magnetic order-disorder transformation (antiferromagnetic to paramagnetic), is apparent from the heat capacity data at similar to673 K for SmFeO3(s) and at similar to560 K for Sm3Fe5O12(S). Enthalpy increment data for SmFeO3(s) and SM3Fe5O12(s), except in the vicinity of X-transition, can be represented by the following polynomial expressions: {H-m(0)(T) - H-m(0)(298.15 K){/J mol-(1)(+/-1.2%) = -54 532.8 + 147.4 . (T/K) + 1.2 . 10(-4) . (T/K)(2) +3.154 . 10(6) . (T/K)(-1); (298.15 less than or equal to T/K less than or equal to 1000) for SmFeO3(s), and {H-m(0)(T) - H-m(0)(298.15 K)}/J mol(-1) (+/-1.4%) = -192 763 + 554.7 . (T/K) + 2.0 . 10(-6) . (T/K)(2) + 8.161 . 10(6) - (T/K)(-1); (298.15 less than or equal to T/K less than or equal to 1000) for Sm3Fe5O12(s). The reversible emf of the solid-state electrochemical cells, (-)Pt/{SmFeO3(s) + Sm2O3(S) + Fe(s)) // YDT / CSZ // {Fe(s) + Fe0.95O(s)} / Pt(+) and (-)Pt/{Fe(s) + Fe0.95O(S)} // CSZ // {SmFeO3(s) + Sm3Fe5O12(s) + Fe3O4(s) / Pt(+), were measured in the temperature ranges of 1005-1259 K and 1030-1252 K, respectively. The standard molar G of formation of solid SmFeO3 and Sm3Fe5O12 calculated by the least squares regression analysis of the data obtained in the current study, and data for Fe0.95O and Sm2O3 from the literature, are given by: Delta(f)G(m)(0)(SmFeO3, s)/kj . mol(-1)(+/-2.0) = -1355.2 + 0.2643 . ; (1005 less than or equal to T/K less than or equal to 1570) and Delta(f)G(m)(0)(Sm3Fe5O12, s)/kj . mol(-1) (+/- 3.1) = -4891.0 + 1.0312 . (T/K); (1030 less than or equal to T/K less than or equal to 1252) The uncertainty estimates for Delta(f)G(m)(0) include the standard deviation in the emf and uncertainty in the data taken from the literature. Based on these thermodynamic data, the oxygen potential diagram for the system Sm-Fe-O was constructed at 1250 K.

ENDOR studies of hydrogen bonding of the AsO44- centre in x-ray irradiated KH2AsO4

We here report what we believe to be an important method for studying hydrogen bonding in systems containing a paramagnetic centre. The technique of electron-nuclear double resonance ( ENDOR) has been applied to study the hydrogen-bond network around the AsO44-. centre in X-ray irradiated KH2AsO4. ENDOR transitions from several sets of hydrogen nuclei surrounding the centre were observed at 4.2 degrees K and the spectra for two sets of neighbouring nuclei are identified. The angular dependences for these spectra are fitted with a spin-Hamiltonian to obtain the isotropic and anisotropic magnetic hyperfine constants. The results are discussed in terms of the available spectroscopic and crystallographic data on KH2AsO4 and the order-disorder model of ferroelectrictricity in this class of crystals.

Beyond the ``Coffee Ring'': Re-entrant Ordering in an Evaporation-Driven Self-Assembly in a Colloidal Suspension on a Substrate

We study the phenomenon of evaporation-driven self-assembly of a colloid suspension of silica microspheres in the interior region and away from the rim of the droplet on a glass plate. In view of the importance of achieving a large-area, monolayer assembly, we first realize a suitable choice of experimental conditions, minimizing the influence of many other competing phenomena that usually complicate the understanding of fundamental concepts of such self-assembly processes in the interior region of a drying droplet. Under these simplifying conditions to bring out essential aspects, our experiments unveil an interesting competition between ordering and compaction in such drying systems in analogy to an impending glass transition. We establish a re-entrant behavior in the order disorder phase diagram as a function of the particle density, such that there is an optimal range of the particle density to realize the long-range ordering. The results are explained with the help of simulations and phenomenological theory.

Dielectric and Raman investigations of structural phase transitions in (C2H5NH3)(2)CdCl4

Temperature-dependent Raman and dielectric measurements have been carried out on (C2H5NH3)(2)CdCl4 single crystals. Raman studies reveal the presence of two structural phase transitions below room temperature at 216 K and 114 K. The phase transitions are marked by anomalies in temperature dependence of wave-number and full width half maximum (FWHM) of several vibrational modes. The transitions are also accompanied by anomalies in dielectric measurements. Raman and dielectric data indicate that the transition at 216 K is order-disorder in nature and is driven by re-orientation of organic ions, while the transition at 114 K is due to coupling between the CdCl6 octahedron and the organic chain. Further high temperature dielectric measurements reveal the presence of one more structural phase transition around 473 K across which dispersion in dielectric parameters is observed. The activation energies and relaxation time obtained for high temperature dielectric phases are characteristic of combined reorientation motions of alkyl ammonium cations.

Influence of grain boundary on melting

The temperature behaviour of an Al bicrystal with surfaces consisting of (110) and (111) crystals is simulated using molecular dynamics. The result shows that the (110) crystal losses its crystalline order at 820K, whereas the disorder does not propagate through the (111) crystal at this temperature. Instead, some disordered atoms are recrystallized into the (111) crystal and the initial grain boundary changes into a stable order-disorder interface. Thus, it was discovered that at a temperature near its melting point, the (111) crystal grew and obstructed the propagation of disorder. Such an obstruction is helpful for understanding melting.

Studies on the phase diagram of the surfactant/1-pentanol water ternary system II: The liquid crystalline phase

The phase behavior of liquid crystalline in the ternary system of dodecyl dimethyl ammonium hydroxyl propyl sulfonate(DDAHPS)/1-pentanol(C5H11OH)/water deuteron (D2O) has been investigated by polarizing optical microscopy, H-2 NMR spectroscopy methods. The results indicate that two kinds of liquid crystals (the lamellar, and the hexagonal) exist in the liquid crystalline phase region. In this paper, we also use the polarized Raman spectroscopy method to measure the values of the order/disorder parameters and the values of the environment polarity parameters for the samples selected from the liquid crystalline phase region, and compare these two parameters of the samples with those of solid state DDAHPS and liquid state pentan-1-ol.

较高阶非线性抽运-探测过程中的空间效应

在飞秒抽运一探测光谱技术中，空间分辨的探测光信号反映了在不同空间位置的材料的非线性效应。当抽运光强度增大时，探测光信号中会出现明显的高阶特别是五阶非线性效应。利用劈裂算子方法直接解决了一维非线性传播方程的问题。在数值模拟中，研究了在不同抽运强度和位置下的抽运一探测过程中的五阶非线性效应。在足够高的抽运场下，探测信号出现清晰的振荡，显示了三阶和五阶非线性效应之间的干涉。当空间位置离抽运场中心足够远时，五阶比三阶非线性效应的衰减快得多，对其物理机制和趋势进行了定性的讨论。

Molecular biomarkers and toxic consequences of impact by organic pollution in aquatic organisms

Organic contaminants are readily bioaccumulated by aquatic organisms. Exposure to and toxic effects of contaminants can be measured in terms of the biochemical responses of the organisms (i.e. molecular biomarkers). The hepatic biotransformation enzyme cytochrome P4501A (CYP1A) in vertebrates is specifically induced by organic contaminants such as aromatic hydrocarbons, PCBs and dioxins, and is involved in chemical carcinogenesis via catalysis of the covalent binding of organic contaminants to DNA (DNA-adducts). Hepatic CYP1A induction has been used extensively and successfully as a biomarker of organic contaminant exposure in fish. Fewer but equally encouraging studies in fish have used hepatic bulky, hydrophobic DNA-adducts as biomarkers of organic contaminant damage. Much less is known of the situation in marine invertebrates, but a CYPlA-like enzyme with limited inducibility and some potential for biomarker application is indicated. Stimulation of reactive oxygen species (ROS) production is another potential mechanism of organic contaminant-mediated DNA and other damage in aquatic organisms. A combination of antioxidant (enzymes, scavengers) and pro-oxidant (oxidised DNA bases, lipid peroxidation) measurements may have potential as a biomarker of organic contaminant exposure (particularly those chemicals which do not induce CYP1A) and/or oxidative stress, but more studies are required. Both CYP1A- and ROS-mediated toxicity are indicated to result in higher order deleterious effects, including cancer and other aspects of animal fitness.