A method and program for mass quantum chemical calculations of protein—ligand docking complexes

A new fast computational method for mass calculations of docking complexes by the AM1/PM3 semiempirical methods is proposed. The computation time is shortened by at least an order of magnitude compared to alternative schemes of quantum chemical calculations. The root-mean-square deviation of the AM1 calculated energies of formation of complexes from the results obtained by conventional diagonalization procedure is at most 0.4 kcal mol⁻¹. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 418–420, February, 2008.     

Permeability,permselectivity, and penetrant‐induced plasticization in fluorinated polyimides studied by positron lifetime measurements

The ortho‐positronium (o‐Ps) lifetime τ₃ and its intensity I₃ in various fluorinated polyimides were determined by the positron annihilation technique and were studied with the spin–lattice relaxation time T₁ and the propylene permeability, solubility, diffusivity, and permselectivity for propylene/propane in them. τ₃, I₃, and the distribution of τ₃ changed when the bulky moieties in the polyimides were changed. The polyimides, having both large τ₃ and I₃ values, exhibited a short T₁ and a high permeability with a low permselectivity. The propylene permeability and diffusivity were exponentially correlated with the product of I₃ and the average free‐volume hole size estimated from τ₃. In highly plasticized states induced by the sorption of propylene, the permeability increased with the propylene pressure in excellent agreement with the change in the free‐volume hole properties probed by o‐Ps. The large and broad distribution of the free‐volume holes and increased local chain mobility for the 2,2‐bis(3,4‐decarboxyphenyl) hexafluoropropane dianhydride‐based polyimides are thought to be important physical properties for promoting penetrant‐induced plasticization. These results suggest that o‐Ps is a powerful probe of not only the free‐volume holes but also the corresponding permeation mechanism and penetrant‐induced plasticization phenomenon. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 308–318, 2003     

Rotational Motion of a Solute Molecule in a Highly Viscous Liquid Studied byC NMR: 1,3-Dibromoadamantane in Polymeric Chlorotrifluoroethene

The viscosity-dependent retarding effect of a polymeric solvent on the rotation of small solute molecules is investigated by¹³C NMR relaxation measurements. It is found that the relaxation data of 1,3-dibromoadamantane in highly viscous polymeric chlorotrifluoroethene can be explained neither by isotropic nor by realistic anisotropic tumbling in a single environment. The experimental data are rationalized in terms of fast exchange between at least two environments with correlation times differing by up to two orders of magnitude. The study shows that a uniform retardation of molecular tumbling by a polymeric solvent, desirable for shifting the NMR observation window in studies of intramolecular mobility, is not always feasible.     

Effect of reaction conditions on the molecular weight and polydispersity of linear poly(arylene ether phosphine oxide)s prepared from an AB monomer

A thorough study of the polymerization behavior of 4‐fluoro‐4′‐hydroxytriphenyl‐phosphine oxide, 2 , under nucleophilic aromatic substitution reactions has been carried out. The synthesis of 2 was achieved in excellent yields by the reaction of bis(4‐fluorophenyl)phenylphosphine oxide, 1 , with one equivalent of potassium hydroxide in DMSO/water. The structure and purity of 2 were confirmed via ¹H, ¹³C, and ³¹P NMR spectroscopy along with elemental analysis. Polymerization reactions of 2 in NMP or DMSO at 180 °C provided the corresponding linear poly(arylene ether phosphine oxide)s, PAEPOs, with number average molecular weights, M_n, ranging from 11,700 to 36,500 Da. All of the polymer samples were completely soluble in chloroform, tetrahydrofuran, DMSO, NMP, and DMAc. The polymerization reactions were accompanied by a competing intramolecular process that resulted in the formation of cyclic oligomeric species that were removed via a final precipitation from methanol. Analysis using ³¹P NMR spectroscopy and size exclusion chromatography (SEC) confirmed that the majority of the lower molecular weight cyclic species were removed via this process. The polymer samples formed tough films when chloroform solutions were slowly evaporated on a glass slide. The PAEPO samples prepared in this study exhibited excellent thermal stability with T_d (5%) values between 503 and 542 in air while the glass transition temperatures ranged from 223 to 237 °C. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 2099–2106, 2006     

Effect of stoichiometry on liquid crystalline supramolecular polymers formed with complementary nucleobase pair interactions

We report herein studies on the liquid crystalline behavior of a series of supramolecular materials that contain different ratios of two complementary symmetrically-substituted alkoxy-bis(phenylethynyl)benzene AA- and BB-type monomers. One monomer has thymine units placed at either end of the rigid mesogenic core, while the other has N⁶-(4-methoxybenzoyl)-adenine units placed on the ends. Differential scanning calorimetric and polarized optical microscopy studies have been carried out on these systems. These studies show that the material's behavior is strongly dependent on its thermal history. As a result, the materials can exhibit, on heating, either a liquid crystalline phase, a crystalline phase, or the coexistence of crystalline and liquid crystalline regions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5049–5059, 2006     

Synthesis of polyacrylonitrile via reverse atom transfer radical polymerization catalyzed by FeCl3/isophthalic acid

FeCl₃ coordinated by isophthalic acid was first used as a catalyst in the azobisisobutyronitrile‐initiated reverse atom transfer radical polymerization of acrylonitrile. N,N‐Dimethylformamide was used as a solvent to improve the solubility of the ligand. An FeCl₃‐to‐isophthalic acid ratio of 0.5 not only gave the best control of the molecular weight and its distribution but also provided rather a rapid reaction rate. The effects of different solvents on the polymerization of acrylonitrile were also investigated. The rate of the polymerization in N,N‐dimethylformamide was faster than that in propylene carbonate and toluene. The molecular weight of polyacrylonitrile agreed reasonably well with the theoretical molecular weight in N,N‐dimethylformamide. The rate of polymerization increased with increasing polymerization temperature, and the apparent activation energy was calculated to be 59.9 kJ mol^?1. Reverse atom transfer radical polymerization was first used to successfully synthesize acrylonitrile polymers with a molecular weight higher than 80,000 and a narrow polydispersity as low as 1.22. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 219–225, 2006