Molecular dynamics study on the phase diagrams of linear and branched chain molecules

The particle transfer molecular dynamics is used to study the phase equilibria of linear and branched chain molecules. The scaling of the critical temperature versus chain length is obtained and the critical densities are found to decrease with increasing chain length, which are in agreement with the results of experiment and theory. The phase diagrams of the linear and the branched chain molecules nearly overlap with each other. Moreover, the radial distribution functions of linear and branched chain molecules in gas phase are very similar, but in the liquid phase, they are different for different kinds of chains.

The electrochemical behavior of a system with a limited number of molecules

In this paper, based on Einstein relationship between diffusion and random walk, the electrochemical behavior of a system with a limited number of molecules was simulated and explored theoretically. The transition of the current vs time responses from discrete to continuous was clearly obtained as the number of redox molecules increased from 10 to 10(6).

Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: More water molecules released

The natural occurrence of the human telomeric G-quadruplex or i-motif in vivo has not been demonstrated and the biological effects of the induction of these structures need to be clarified. Intracellular environments are highly crowded with various biomolecules and in vitro studies under molecular-crowding conditions will provide important information on how biomolecules behave in cells. Here we report that cell-mimic crowding can increase i-motif stability at acid pH and cause dehydration.

Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry

The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA, however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded).

Monitoring catalytic degradation of dye molecules on silver-coated ZnO nanowire arrays by surface-enhanced Raman spectroscopy

Catalytic degradation of organic dye molecules has attracted extensive attention due to their high toxicity to water resources. In this paper, we propose a novel method for the fabrication of uniform silver-coated ZnO nanowire arrays. The degradation of typical dye molecule rhodamine 6G (R6G), as an example, is investigated in the presence of the as-prepared silver-coated ZnO nanowire arrays. The experimental results show that such composite nanostructures exhibit high catalytic activity, and the reaction follows pseudo-first-order kinetics. Furthermore, these nanowire arrays are desirable SERS substrates for monitoring the catalytic degradation of dye molecules. Compared with traditional UV-visible spectroscopy, SERS technology can reflect more truly the catalytic degradation process occurring on the surface of the catalysts.

Magnetic Coupling between Copper(II) Ions Mediated by Hydrogen-Bonded (Neutral) Water Molecules

A new hydrogen-bonded dinuclear copper(II) coordination compound has been synthesized from the Schiff-base ligand 6-(pyridine-2-ylhydrazonomethyl)phenol (Hphp). The molecular structure of [Cu-2(php)(2)(H2O2)(2)(ClO4)](ClO4)- (H2O) (1), determined by single-crystal X-ray diffraction, reveals the presence of two copper(II) centers held together by means of two strong hydrogen bonds, with O center dot O contacts of only 2.60-2.68 angstrom. Temperature-dependent magnetic susceptibility measurements down to 3 K show that the two metal ions are antiferromagnetically coupled (J = -19.8(2) cm(-1)). This exchange is most likely through two hydrogen-bonding pathways, where a coordinated water on the first Cu, donates a H bond to the O atoms of the coordinated php at the other Cu. This strong O center dot H (water) bonding interaction has been clearly evidenced by theoretical calculations. In the relatively few related cases from the literature, this exchange path, mediated by a (neutral) coordinated water molecule, was not recognized.

Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

Reusable, label-free electrochemical aptasensor for sensitive detection of small molecules

We report a sensitive electrochemical aptasensor for adenosine based on electrochemical impedance spectroscopy measurement, which gives not only a label-free but also a reusable platform to make the detection of small molecules simple and convenient.

Surface plasmon resonance and electrochemistry for detection of small molecules using catalyzed deposition of metal ions on gold substrate

Small molecules are difficult to detect by conventional surface plasmon resonance (SPR) spectroscopy due to the fact that the changes in the refractive index resulted from the binding process of small biomolecules are quite small. Here, we report a simple and effective method to detect small biomolecule using SPR spectroscopy and electrochemistry by catalyzed deposition of metal ions on SPR gold film. As an example, the ascorbic acid-mediated deposition of Ag on gold film was monitored by in situ SPR spectrum. The deposition of Ag atom on gold film resulted in an obvious decrease of depth in SPR angular scan curves of reflectance intensity and minimum reflectivity angle. The depth change of the SPR reflectance intensity and minimum reflectivity angle curves mainly relied on the amount of Ag atom deposited on gold film that can be controlled by the concentration of ascorbic acid. By monitoring the deposition of Ag atom on gold film, ascorbic acid was detected in the concentration range of 2 x 10(-5) M to 1 x 10(-3) M. After each of detections, the SPR sensor surface was completely regenerated by a potential step that stripped off the Ag atom. Furthermore, the regeneration process of the sensor surface provides the feasibility for detecting the concentration of ascorbic acid by electrochemical method.

Sugars-grafted aliphatic biodegradable poly(L-lactide-co-carbonate)s by click reaction and their specific interaction with lectin molecules

A novel biodegradable aliphatic poly(L-lactide-co-carbonate) bearing pendant acetylene groups was successfully prepared by ring-opening copolymerization of L-lactide (LA) with 5-methyl-5-propargyloxycarbonyl-1,3-dioxan-2-one (PC) in the presence of benzyl alcohol as initiator with ZnEt2 as catalyst in bulk at 100 degrees C and subsequently used for grafting 2-azidoethyl beta-D-glucopyranoside and 2-azidoethyl beta-lactoside by the typical "click reaction," that is Cu(I)-catalyzed cycloaddition of azide and alkyne. The density of acetylene groups in the copolymer can be tailored by the molar ratio of PC to LA during the copolymerization. The aliphatic copolymers grafted with sugars showed low cytotoxicity to L929 cells, improved hydrophilic properties and specific recognition and binding ability with lectins, that is Concanavalin A (Con A) and Ricinus communis agglutinin (RCA). Therefore, this kind of sugar-grafted copolymer could be a good candidate in variety of biomedical applications.

Manipulations of atoms and molecules by scanning probe microscopyk

Scanning probe microscopy (SPM), including scanning tunneling microscopy (STM) and atomic force microscopy (AFM), has become a powerful tool in building nanoscale structures required by modern industry. In this article, the use of SPM for the manipulation of atoms and molecules for patterning nanostructures for opt-electronic and biomedical applications is reviewed. The principles and procedures of manipulation using STM and AFM-based technologies are presented with an emphasis on their ability to create a wide variety of nanostructures for different applications. The interaction among the atoms/molecules, surface, and tip are discussed. The approaches for positioning the atom/molecule from and to the desired locations and for precisely controlling its movement are elaborated for each specific manipulation technique. As an AFM-based technique, the dip-pen nanolithography is also included. Finally, concluding remarks on technological improvement and future research is provided.

Electronic structures of MCO (M = Nb, Ta, Rh, Ir, Pd, Pt) molecules by density functional theory

Equilibrium geometries, vibrational frequencies, and dissociation energies of the transition metal carbonyls MCO (M = Nb, Ta, Rh, Ir, Pd, Pt) were studied by use of diverse density functional methods B3LYP, BLYP, B3P86, B3PW91, BHLYP, BP86, and PBE1PBE. It was found that the ground electronic state is (6)Sigma(+) for NbCO and TaCO, (2)Sigma(+) for RhCO,(2)Delta for IrCO, and (1)Sigma(+) for PdCO and PtCO, in agreement with previous theoretical studies. The calculated properties are highly dependent on the functionals employed, in particular for the dissociation energy. For most of the molecules, the predicted bond distance is in agreement with experiments and previous theoretical results. BHLYP is the worst method in reproducing the experimental results compared with the other density functional methods for the title molecules.