Do orientation effects contribute to the molecular weight dependence of the free solution mobility of DNA?

The free solution mobility of DNA increases with increasing molecular weight and then levels off and becomes constant at molecular weights above approximately 400 bp (Stellwagen, N. C., Gelfi, C., Righetti, P. G., Biopolymers 1997,42, 687-703). To investigate whether the increase in mobility could be attributed to an increased orientation of the larger DNA molecules in the electric field, the free solution mobility of DNA was measured by capillary electrophoresis as a function of electric field strength. Mixtures containing 20-, 118- and 422-bp DNA molecules, and 20-, 422- and 2116-bp DNAs, were studied. If the larger DNA molecules in each mixture were oriented by the electric field, their mobilities should increase with electric field strength faster than the mobility of the 20-bp oligomer, which is too small to be oriented by the electric fields used in this study. Instead, the ratios of the mobilities of the 118-, 422- and 2116-bp fragments to the mobility of the 20-bp oligomer were independent of electric field strength. Hence, orientation effects are not important for DNA molecules up to 2 kbp in size, in electric fields up to 500 V/cm in amplitude. An explanation is suggested.     

Do molecular conductances correlate with electrochemical rate constants? Experimental insights

We measured single-molecule conductances for three different redox systems self-assembled onto gold by the STMBJ method and compared them with electrochemical heterogeneous rate constants determined by ultrafast voltammetry. It was observed that fast systems indeed give higher conductance. Monotonous dependency of conductance on potential reveals that large molecular fluctuations prevent the molecular redox levels to lie in between the Fermi levels of the electrodes in the nanogap configuration. Electronic coupling factors for both experimental approaches were therefore evaluated based on the superexchange mechanism theory. The results suggest that coupling is surprisingly on the same order of magnitude or even larger in conductance measurements whereas electron transfer occurs on larger distances than in transient electrochemistry.     

On the scaling law of the evolution of lap-shear strength with healing temperature at amorphous polymer−polymer interfaces and surface glass transition

The evolution of lap-shear strength (σ) with healing temperature T _h at symmetric and asymmetric amorphous polymer−polymer interfaces formed of the samples with vitrified bulk has been investigated. It has been found that the square root of the lap-shear strength behaves with respect to healing temperature as σ ^1/2 ~ T _h both at symmetric and asymmetric interfaces. Basing on this scaling law between σ and T _h, the values of the surface glass transition temperature ( T_g^surface ) \left( {T_{\rm{g}}^{\rm{surface}}} \right) have been estimated for a number of amorphous polymers by the extrapolation of the experimental curves σ ^1/2 ~ T _h for symmetric polymer−polymer interfaces and, in some cases, for asymmetric, both compatible and incompatible, polymer−polymer interfaces, to zero strength. A significant reduction in surface glass transition temperature T_g^surface T_{\rm{g}}^{\rm{surface}} with respect to the glass transition temperature of the polymer bulk ( T_g^bulk ) \left( {T_{\rm{g}}^{\rm{bulk}}} \right) , reported earlier, has been confirmed by the use of the new proposed approach. The quasi-equilibrium surface glass transition temperature T_g^surface T_{\rm{g}}^{\rm{surface}} of amorphous polystyrene (PS) has been predicted in the framework of an Arrhenius approach using the plot “logarithm of healing time − reciprocal surface glass transition temperature T_g^surface￠￠ T_{\rm{g}}^{\rm{surface}}\prime \prime and the activation energy of the surface alpha-relaxation of PS has been calculated.     

Effect of heating rate on the sinterability,crystallization, and mechanical properties of sintered glass–ceramics from granite waste

Huge amounts of granite wastes have been generated in the granite-processing industry and should be properly disposed to reduce the negative impacts on the environment and health care. In this work, waste granite powder was modified and sintered to prepare high-strength and tough glass–ceramics. The heating rate was studied to clarify its effects on the sinterability, crystallization, and mechanical properties of glass–ceramics. With the increase in heating rate, the densification of sintered glass–ceramics was promoted by the liquid glassy phase from the microcline phase. The glass–ceramics were strengthened and toughened simultaneously due to the improved densification and increased crystallinity. The toughening mechanism was attributed to the crack bridging, deflection, and branching. The maximum flexural strength of 143 MPa and fracture toughness of 2.1 MPa m^1/2 were achieved with a heating rate of 50 °C min⁻¹, far superior to that of natural granite. The crystal structure of sintered glass–ceramics indicated the main crystalline phase of anorthite. These glass–ceramics with excellent mechanical properties promise the practical reutilization of granite wastes in the construction tiles.

     

The further crystallographic refinement of trichosanthin at 2.7A resolution and the comparison among the three molecular structures in two crystal forms

The three-dimensional structure of trichosanthin at 2.7A resolution has been improved further, by refitting one of the C-terminal tails, adjusting 16 residues in the molecular surface regions, discarding some water molecules with high B values, and adjusting weights during the further refinement. The R-factor has been reduced to 18.5% and the r.m.s deviations from ideal geometry are also improved. The structures of the two molecules in the monoclinic asymmetric unit and the only molecule in the orthorhombic asymmetric unit are compared with one another. The main-chain structures for most of the residues in the three molecules are substantially the same. However, the courses of the three C-terminal tails are completely different, and the intermolecular interactions resulting from the particular packing of the molecules in the crystals account for the differences. The strand Be-2 and the preceding B-turn in small domain show large r.m.s. deviations among the three molecules and they are also involved in i     

Do polysaccharides such as dextran and their monomers really increase the surface tension of water?

It has been reported in the literature that sugars such as dextrose and sucrose increase the surface tension of water. The effect was interpreted as a depletion of the solute molecules from the water-air interface. This paper presents accurate measurements of the surface tension of different concentrations of dextrose solution as well as its polymer (i.e., dextran). An automated drop shape technique called axisymmetric drop shape analysis (ADSA) was used for the surface tension determination. The surface tension measurement is presented as a function of a shape parameter, P(s), which has been used to quantify the range of the applicability of ADSA. The results of the above study show that dextrose solutions decrease the surface tension of water in contradiction to the results obtained from the weight drop method in the literature. The surface tension decreases continuously with increasing concentration. A similar effect was observed for the dextran solutions. To verify that the setup and the methodology are capable of accurately measuring increases in surface tension, a similar experiment was conducted with a sodium chloride solution with a concentration of 1 M. It is well-known that electrolyte solutions, e.g., sodium chloride, increase the surface tension of water. The results obtained from ADSA verify that the sodium chloride increases the surface tension of water by 1.6 mJ/m(2). It is concluded that dextrose and dextran decrease the surface tension of water. Thus, there is no evidence of depletion. To identify the sources of discrepancy between the results of ADSA and those reported in the literature, the experiments were repeated for different concentrations and the rate of drop formation using the drop weight method. It was found that the rate of drop formation is most likely the source of error in the results reported in the literature.     

Evaluation of a novel silica-supported sol–gel sorbent prepared by a surface molecular imprinting technique for the selective separation of estazolam from human plasma

A molecular imprinting polymer (MIP) based on surface modification of silica gel was prepared via the sol–gel process with 3-aminopropyltriethoxysilane and phenyltrimethoxysilane as functional monomers, and estazolam as the template. The imprinted silica sorbent was characterized by Fourier Transform Infrared Spectroscopy, surface elemental analysis, and scanning electron microscopy (SEM). An MIP of agglomerated nano-particles with multi-pores was grafted onto the surface of the silica gel after hydrolytic condensation of the siloxane. The imprinted silica sorbent was used for solid phase extraction (SPE). Using water as loading solvent, the extraction efficiency for estazolam was higher compared to the use of an organic solvent. The imprinted silica sorbent was selective not only for the template, but also for the analogue. Compared to C₁₈-SPE and liquid–liquid extraction, the MIP-SPE was the most feasible technique for extraction of estazolam from human plasma; up to 98.7?±?1.2% recovery was achieved.     

Crystal and molecular structures of two polymorphs of a furanocoumarin — Smyrindiol from Smyrniopsis aucheri

The structures of two polymorphic modifications (I) and (II), of a furocoumarin — smyrindiol fromSmyrniopsis aucheri — have been determined by the x-ray structural method. Polymorph I, isolated from the earlier fraction, differed from polymorph II by the presence of a solvate acetone molecule in the crystal. The conformations of the smyrindiol molecule in the two polymorphs differed slightly in the furan ring.     

Volatile organic compound adsorption on a nonporous silica surface: how do different probe molecules sense the same surface?

In this work, we compare experimental results to molecular simulation results of volatile organic compound (VOC) adsorption on nonporous silica. We adopted an effective model for the rough solid surface, obtained by a temperature annealing scheme, plus an experimental/simulation nitrogen adsorption tuning process over the silica energetic oxygen parameter. The measurement/prediction of selected VOCs, specifically, n-pentane and methylcyclohexane, is presented in terms of adsorption isotherms, with an emphasis on the angle distribution analysis of the three studied probe molecules with respect to the same modeled surface.     

Do all the protic ionic liquids exist as molecular aggregates in the gas phase?

According to an EI-MS study of 1,1,3,3-tetramethylguanidium-based protic ionic liquids (PILs), it has been concluded that not all PILs exist as molecular aggregates in the gas phase. The detection of both ions of m/z 115.0 and m/z 116.0 for the 1,1,3,3-tetramethylguanidinium trifluoromethylsulfonate (TMGS) protic ionic liquid indicates that both the molecular and ionic aggregates co-exist in the gas phase, which is to say that the TMGS may also evaporate via the ionic aggregates just like aprotic ionic liquids. Furthermore, investigation on triethylamine-based and 1-methylimidazole-based PILs confirmed that the gas phase structure of PILs depends on both the acidity and basicity of the corresponding acid and base.     

Conformation and rotational mobility ofэSiOĊH2 radicals grafted onto the silica surface

The conformation ofэSiOC·H₂ radicals was determined by comparison of the ESR data and results of quantum-chemical calculations. Based on the experimental data, the characteristic times τ_c of rotational mobility ofэSiOC·H₂ radicals grafted onto a silica surface were estimated over the temperature interval from 77 (τ_c = 15.8 · 10^-8 s) to 295 K (τ_c 1.3 · 10^-8 s). Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2092–2095, November, 1999.     

Effects of stereo-defect distribution and molecular mass in the non-isothermal crystallization behavior of β-nucleated isotactic polypropylene

In this study, based on the synthesis of two Ziegler–Natta iPP with nearly same average isotacticity but different uniformities of stereo-defect distribution, we further prepared two series of β-iPP with different molecular masses by addition of different concentration of peroxide. We investigated the combination effects of stereo-defect distribution and molecular mass on the non-isothermal crystallization behavior and polymorphic composition behavior of β-iPP by differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD), and scanning electron microscope (SEM). The results of non-isothermal crystallization kinetics revealed that the iPP molecular mass has only slight influence on the crystallization temperature of β-iPP, while the uniformity of stereo-defect distribution not only evidently influences the crystallization temperature, but also affects the dependency of crystallization temperature on cooling rate. β-iPP with less uniformity of stereo-defect distribution leads to higher dependency of crystallization temperature on the cooling rate. The calculation of crystallization activation energy ΔE showed that the lower the molecular mass, the lower the ΔE, indicating that it is easier for the occurrence of crystallization. Meanwhile, iPP with more uniform stereo-defect distribution has lower ΔE. Moreover, both stereo-defect distribution and molecular mass are important factors in determining the polymorphic composition. A more uniform stereo-defect distribution is more favorable for the β-phase crystallization; the lower the molecular mass, the harder for β-phase crystallization to take place. However, compared with iPP molecular mass, the uniformity of stereo-defect distribution is the first-order factor in determining the β-phase crystallization of iPP. Moreover, the thermal stability and the dependency of β-phase proportion on the cooling rate are also found to be highly dependent on the iPP molecular mass.     

Do vectors point the way to understanding energy transfer in molecular collisions?

This tutorial review examines the proposition that vector properties reveal more about the underlying potential energy surfaces controlling the inelastic exchange of energy in intermolecular collisions than conventional scalar measurements. Exciting recent experimental progress is summarized in the form of six selected cases studies. The new information that has been extracted is compared with the predictions of complementary theory. Likely future prospects and promising avenues for further progress are discussed. The treatment should appeal to all those with interests in the forces governing intermolecular interactions, especially in gas-phase collisions.     

Low-temperature dynamics in amorphous polymers and low-molecular-weight glasses--what is the difference?

Numerous experiments have shown that the low-temperature dynamics of a wide variety of disordered solids is qualitatively universal. However, most of these results were obtained with ensemble-averaging techniques which hide the local parameters of the dynamic processes. We used single-molecule (SM) spectroscopy for direct observation of the dynamic processes in disordered solids with different internal structure and chemical composition. The surprising result is that the dynamics of low-molecular-weight glasses and short-chain polymers does not follow, on a microscopic level, the current concept of low-temperature glass dynamics. An extra contribution to the dynamics was detected causing irreproducible jumps and drifts of the SM spectra on timescales between milliseconds and minutes. In most matrices consisting of small molecules and oligomers, the spectral dynamics was so fast that SM spectra could hardly or not at all be recorded and only irregular fluorescence flares were observed. These results provide new mechanistic insight into the behavior of glasses in general: At low temperatures, the local dynamics of disordered solids is not universal but depends on the structure and chemical composition of the material.     

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

Aggregation of amyloid-β (Aβ) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between Aβ protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in Aβ(17-42) protofibril. It is found that the nonpolar interactions are the important forces to stabilize the Aβ(17-42) protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the Aβ(17-42) are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of Aβ as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between Aβ monomers in Aβ(17-42) protofibril, and the findings are considered critical for exploring effective agents for the inhibition of Aβ aggregation.     

Different binding orientations for the same agonist at homologous receptors: a lock and key or a simple wedge?

Using unnatural amino acid mutagenesis, the binding site for serotonin at the novel Caenorhabditis elegans receptor MOD-1 has been probed. As with the closely related serotonin receptor 5-HT3, MOD-1 makes use of a strong cation-pi interaction between the ammonium of serotonin and the indole side chain of a tryptophan. However, the specific Trp used by MOD-1 is different from that used for 5-HT3 (and the nAChR), aligning with a residue more than 40 amino acids distant in sequence space and on a different "loop" of the agonist binding site. This suggests a significant rearrangement of the ligand on binding these two closely related receptors. It is suggested that, unlike enzymes, receptors and other signaling molecules may need only to deliver an agonist to a general binding region, rather than establishing precise drug-receptor interactions.     

How does the mobility of phospholipid molecules at a water/oil interface reflect the viscosity of the surrounding oil?

The mobility of phospholipid molecules at a water/oil interface on cell-sized phospholipid-coated microdroplets was investigated through the measurement of diffusion constants by fluorescence recovery after photobleaching. It is found that the diffusion constant of phospholipids showed the relation D approximately (eta water + eta oil) -0.85, where D is the diffusion constant, eta water is the viscosity of water, and eta oil is the viscosity of oil. This observation indicates that the viscosity of the surrounding oil is the primary factor that determines the diffusibility of phospholipids at a water/oil interface.     

Directing the secondary structure of polypeptides at will: from helices to amyloids and back again?

An ageing society faces an increasing number of neurodegenerative diseases such as Alzheimer's, Parkinson's, and Creutzfeld-Jacob disease. The deposition of amyloid fibrils is a pathogenic factor causing the destruction of neuronal tissue. Amyloid-forming proteins are mainly alpha-helical in their native conformation, but undergo an alpha-helix to beta-strand conversion before or during fibril formation. Partially unfolded or misfolded beta-sheet fragments are discussed as direct precursors of amyloids. To potentially cure neurodegenerative diseases we need to understand the complex folding mechanisms that shift the equilibrium from the functional to the pathological isoform of the proteins involved. This paper describes a novel approach that allows us to study the interplay between peptide primary structure and environmental conditions for peptide and protein folding in its whole complexity on a molecular level. This de novo designed peptide system may achieve selective inhibition of fibril formation.