Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling

Potential of mean force (PMF) calculations provide a reliable method for determination of the absolute binding free energies for protein-ligand systems. The common method used for this purpose -- umbrella sampling with weighted histogram analysis -- is computationally very laborious, which limits its applications. Recently, a much simpler alternative for PMF calculations has become available, namely, using Jarzynski's equality in steered molecular dynamics simulations. So far, there have been a few comparisons of the two methods and mostly in simple systems that do not reflect the complexities of protein-ligand systems. Here, we use both methods to calculate the PMF for ion permeation and ligand binding to ion channels. Comparison of results indicate that Jarzynski's method suffers from relaxation problems in complex systems and would require much longer simulation times to yield reliable PMFs for protein-ligand systems.     

Di- and tetranuclear copper(II) complexes of a novel binucleating tetrathioether-tetrathiol ligand

A novel bi-tetradentate polythioether ligand, 6,6-methylene-bis(5- mercapto-3-thiahexyl)-4,8-dithiaundecane-1, 11-dithiol (H4L) was synthesized, and its di- and tetranuclear copper(II) complexes were prepared, and characterized by elemental analyses, magnetic moments, 1H-n.m.r., i.r., and Uv/vis spectra. The i.r. data show that the ligand acts in a tetradentate manner and coordinates via one S atom of the thioether and thiol groups. The geometry of the metal chelates is discussed with the help of magnetic and spectroscopic measurements. The elemental analyses, stoichiometry, and spectroscopic data of the complexes indicate that the copper(II) ions are coordinated to the bi-dianion of the ligand. The function of the thiol ligand is to release protons to form copper(II) complexes, (Cu2L).     

Investigation of DNA cleavage activities of new oxime-type ligand complexes and molecular modeling of complex-DNA interactions

Nucleolytic activities of some new oxime-type ligand complexes were investigated by neutral agarose gel electrophoresis. Analysis of the cleavage products in agarose gel indicated that all complexes used converted supercoiled pUC18 plasmid DNA to its nicked or linear form. It was found that nucleolytic activities of the complexes depend on the complex concentration, reaction time and the presence of a cooxidant (magnesium monoperoxyphthalate, MMPP) in the reaction mixture. However, the complexes cleaved pUC18 plasmid DNA at all investigated pH values. Nucleolytic activities of complexes were investigated for different complex concentrations (0.1–100 μmol L⁻¹), pH values (6.0–10.0) and reaction times (0–60 min). Molecular modeling studies performed by the Hyperchem Software together with DNA-binding studies showed that planar sites of the complexes intercalated into double stranded DNA. It can be concluded that all oxime-type ligand complexes used can be evaluated as nuclease mimics.     

Current versus gate voltage hysteresis in organic field effect transistors

Abstract  

Research into organic field effect transistors (OFETs) has made significant advances—both scientifically and technologically—during the last decade, and the first products will soon enter the market. Printed electronic circuits using organic resistors, diodes and transistors may become cheap alternatives to silicon-based systems, especially in large-area applications. A key parameter for device operation, besides long term stability, is the reproducibility of the current–voltage behavior, which may be affected by hysteresis phenomena. Hysteresis effects are often observed in organic transistors during sweeps of the gate voltage (V _GS). This hysteresis can originate in various ways, but comparative scientific investigations are rare and a comprehensive picture of “hysteresis phenomena” in OFETs is still missing. This review provides an overview of the physical effects that cause hysteresis and discusses the importance of such effects in OFETs in a comparative manner.     

Poly(vinylferrocenium) coated disposable pencil graphite electrode for DNA hybridization

Poly(vinylferrocenium) (PVF⁺) modified electrode was developed in this study for the electrochemical sensing of DNA based on the oxidation signals of polymer, adenine and guanine. Experimental parameters, such as; polymeric film thickness, DNA immobilization time and DNA concentration were examined in order to obtain more sensitive and selective electrochemical signals. After optimization studies, DNA hybridization was investigated.     

A Novel Method for the Synthesis of Newfangled Asymmetric Schiff Bases from α‐amino Acids under Ultrasonic Conditions and in Aqueous Medium

Chiral Schiff bases were obtained at high yields via a novel technique. Aryl aldehydes and chiral α‐amino acids were treated (1) in the presence of H₃PO₄ in ethanol at 80°C for 24 h, and (2) in the presence of K₂CO₃ under ultrasonic conditions in an aqueous ethanol medium within 5 min with yields reaching up to 96%. The results showed that the presented methodology under ultrasonic conditions was effective, practical, and eco‐friendly compared to that using an acidic medium. The corresponding asymmetric Schiff bases were synthesized for the first time, and were characterized by ¹H and ¹³C nuclear magnetic resonance and infrared spectroscopy and high‐resolution mass spectrometry.     

FT-IR,FT-Raman spectra and quantum mechanical study of piperidine-3-carboxylic acid and its tautomers,isomers

The mid-IR, far-IR, and Raman spectra of piperidine-3-carboxylic acid were measured and interpreted with support of the MP2 and B3LYP/6-311++G(d, p) calculated harmonic vibrational spectra. 10 stable piperidine-3-carboxylic acid tautomers/isomers were found after B3LYP, calculations. The experimental absorption bands of carboxylate (COO^?) group show that the free piperidine-3-carboxylic acid molecule exists in zwitterionic form and the most stable tautomer (NAT-1) can be stabilized by an intramolecular N-H...O hydrogen bond. All vibrational frequencies of NAT-1 assigned in detail with the help of total energy distribution (TED). The experimental vibrational wave numbers were compared with the calculated data.     

Laser ultrasonic receivers based on organic photorefractive polymer composites

We present two laser ultrasonic receivers based on organic photorefractive polymer composites with 2-[4-bis(2-methoxyethyl)aminobenzylidene]malononitrile (AODCST) or 2-dicyanomethylen-3-cyano-5,5-dimethyl-4-(4′-dihexylaminophenyl)-2,5-dihydrofuran nonlinear optical chromophores. Experimental results show sensitivities of the ultrasonic receivers of ~9.5 × 10^?8 nm (W/Hz)^0.5 for both composites, and a faster response time (~60 ms) for the AODCST-based laser ultrasonic receiver. We show that such LUS detectors are highly suitable for contactless thickness measurements of aluminum, steel sheets and defect detection with an accuracy of 100 μm.     

On-chip optical filters with designable characteristics based on an interferometer with embedded silicon photonic structures

We demonstrate chip-scale flat-top filters at near-IR wavelengths using negative index photonic crystal based Mach-Zehnder interferometers. Supported by full three-dimensional numerical simulations, we experimentally demonstrate a new approach for engineering high-pass, low-pass, bandpass, and band-reject filters, based on designing the photonic band diagram both within the bandgap frequency region and away from it. We further show that our approach can be used to design filters that have tunable multilevel response for different sections of the spectrum and for different polarizations. This configuration enables deterministic control of the bandwidth and the rejection ratio of filters for integrated photonic circuits.