Nanoclusteration of DNA with dendronized polymer in terms of free energy

A thermodynamic cycle for the nanoclusteration between DNA and dendronized polymer is proposed and electrostatic free energies of a series of DNA- dendronized polymer nanoclusteration processes are calculated. The free energies for assembling fixed charges and mobile ions, and the bending energies of the DNA chain wrapped around the dendronized polymer are taken into consideration. The free energies of nanoclusteration are calculated for a number of nanoclusters with different conformations at constant temperature and constant ionic strength. The effects of temperature and ionic strength on the free energy of nanoclusteration and stability of their conformations are also investigated.     

An accurate expression for radial distribution function of the Lennard-Jones fluid

A simple and accurate expression for radial distribution function (RDF) of the Lennard-Jones fluid is presented. The expression explicitly states the RDF as a continuous function of reduced interparticle distance, temperature, and density. It satisfies the limiting conditions of zero density and infinite distance imposed by statistical thermodynamics. The distance dependence of this expression is expressed by an equation which contains 11 adjustable parameters. These parameters are fitted to 353 RDF data, obtained by molecular dynamics calculations, and then expressed as functions of reduced distance, temperature and density. This expression, having a total of 65 constants, reproduces the RDF data with an average root-mean-squared deviation of 0.0152 for the range of state variables of 0.5  T^*  5.1 and 0.35  ρ^*  1.1 (T^*=kT/ε and ρ^* = ρσ³ are reduced temperature and density, respectively). The expression predicts the pressure and the internal energy of the Lennard-Jones fluid with an uncertainty that is comparable to that obtained directly from the molecular dynamics simulations.     

The effects of mechanical properties of DNA on the thermodynamic stability of the DNA-dendronized polymer nanocluster

The effects of the mechanical properties of DNA, such as bending, twisting, and bending-twisting interactions on the thermodynamic stability of DNA-dendronized polymer nanoclusters with different conformations in terms of free energy are investigated. The effect of temperature on the free energy is also studied and the values of enthalpy and entropy of the solution of the nanocluster are predicted. The obtained thermodynamic quantities help us to have a better understanding about the mechanical properties of DNA and the stability of the nanocluster in gene therapy.     

Prediction of Solubility Parameters Based on the Explicit Expression of Statistical Thermodynamics

A robust and efficient procedure is presented for calculating the solubility parameter. An analytical equation for internal pressure is proposed. Through a simple relation reported by Verdier and Andersen (fluid phase equilibrium 231: 125–137, 2005), one can easily find the solubility parameter via our analytical equation for the internal pressure. Also, the radial distribution function (RDF) of a Lennard–Jones LJ (12, 6) fluid, proposed by Xu and Hu (fluid phase equilibrium 30: 221–228, 1986), has been employed to calculate the internal pressure of normal alkanes from methane to decane. Their solubility parameters were evaluated according to the calculated values of the internal pressure. A comparison between the experimental and the estimated values demonstrated a very good agreement between them.     

Development of a new synthesis approach for S-pregabalin by optimizing the preparation stages

Journal of the Iranian Chemical Society - In the present study, we aimed to optimize the synthesis stages of S-pregabalin ((S)-3-(aminomethyl)-5-methylhexanoic acid), a well-known anticonvulsant...     

2-Pyridyl-benzimidazole-Pd(II)/Pd(0) Supported on Magnetic Mesoporous Silica: Aerobic Oxidation of Benzyl Alcohols/Benzaldehydes and Reduction of Nitroarenes

Catalysis Surveys from Asia - 2-(2-Pyridyl)benzimidazole (PyBzIm) was supported onto magnetic mesoporous silica, Fe3O4@SiO2@SBA-15 via the click chemistry. The supported ligand was treated with...     

Binding affinity prediction for binary drug–target interactions using semi-supervised transfer learning

Journal of Computer-Aided Molecular Design - In the field of drug–target interactions prediction, the majority of approaches formulated the problem as a simple binary classification task....     

Kinetics and Mechanism of Izomerization of N-Alkoxycarbonyl-5-aroxytetrazoles

The kinetics and mechanism of the N²-N¹-isomerization of 2-methoxycarbonyl-5-(p-X-phenoxy)- tetrazoles (X = H, CH₃, NHCOCH₃, Cl, Br, NO₂) were studied by ¹H NMR spectroscopy in a DMSO-d ₆-CDCl₃ mixture (25:75). The rate of isomerization of the N²-isomer into N¹-isomer fit the first-order equation (after three half-conversion periods). The isomerization is accompanied by hydrolysis and decarboxylation. The Hammett plot of ln(k _X k _H) for the isomerization showed a good correlation with ^- values (^- = 1.33, r = 0.965). A poor correlation with values was obtained. The kinetic data, the effect of solvent polarity, the substituent effects, and the results of AM1 quantum-chemical calculations suggest an ionic mechanism of the isomerization in polar solvents and a concerted mechanism in nonpolar solvents.     

Aromatic poly(amide-ether)s containing naphthalene and methylene unites

1,5-Naphthene dioxy diacetic acid was synthesized from the reaction of 1,5-naphthalene diol and chloroacetic acid. It was used then as a bi-functiona l monomer in polycondensation reaction with aromatic diamines in the presence of tripnenylphosphite to produce poly(amide-ether)s. All the obtained polymers were characterized by IR and elemental analysis; their solubility behaviour was evaluated in polar organic solvents as well as in concentrated H₂SO₄. The extent of thermal stability and phase transitions of poly(amide- ether)s were investigated by thermogravimetric analysis and differential scanning calorimetry respectively; while the morphology was estimated by X-ray powder diffraction patterns. Besides, the fu-fu stacking character of polymer chain interactions in the solid state was confirmed by absorption spectra of solid thin films.     

Novel polyimides obtained from a new aromatic diamine (BAPO) containing pyridine and 1,3,4‐oxadiazole moieties for removal of Co(II) and Ni(II) ions

Novel, thermally stable polyimides (PIs) containing a 1,3,4‐oxadiazole and pyridine moieties based on a new aromatic diamine 2,5‐bis‐(aminopyridine‐2‐yl)‐1,3,4‐oxadiazole, BAPO, were synthesized. The prepared polymers were soluble in dimethysulfoxide (DMSO) and concentrated sulfuric acid at room temperature as well as in polar and aprotic solvents, such as, N‐methylpyrrolidone (NMP) and N,N‐dimethylacetamide (DMAc) at elevated temperature. Thermal behaviors of the PIs were studied by thermogravimetric analysis/dynamic thermal analysis (TGA‐DTA) and differential scanning calorimetry (DSC). The inherent viscosities of the PI solutions were in the range of 0.38–0.61 dl/g (in DMSO with a concentration of 0.125 g/dl at 25 ± 0.5°C). The removal of Co(II) and Ni(II) ions from aqueous solutions was performed using polymer 6, which was obtained from BAPO and 3,3′,4,4′‐benzophenonetetracarboxylic dianhydride (BTDA). The maximum adsorption capacity was observed for Co(II) ion at pH = 7.0 (110.4 mg g^?1, 1.87 mmol g^?1). Copyright © 2015 John Wiley & Sons, Ltd.