Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV‐1 protease and F‐ATP synthase

We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three‐dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D‐RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI‐272 bound form of HIV‐1 protease and predicting both sodium ions and water molecules near the rotor ring of F‐adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39–0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D‐RISM output within minutes. It is extremely useful for examining multiple specific solvent–solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc.     

Nonlinear electromechanical fields and localized polarization switching of 1-3 piezoelectric/polymer composites

This paper examines the nonlinear electromechanical response of 1-3 piezoelectric/polymer composites. The piezocomposites contain square or circular piezoelectric rods in an epoxy matrix. Experiments were conducted to measure the displacement versus electric field curves, using the device specimen of the 1-3 piezocomposites. Three dimensional finite element analysis was also carried out to study the electromechanical fields in the 1-3 piezocomposites by introducing a model for polarization switching. Comparison was then made between simulation and experiment.     

Solvent effects on conformational stability of peptides: RISM analyses

We describe features of our methodology for predicting tertiary structures (i.e., conformations) of proteins in solvent just from the amino-acid sequences and molecular models for the solvent. The methodology, which is a combination of the Monte Carlo simulated annealing technique and the reference interaction site model theory, is illustrated for the small peptides, Met-enkephalin and C-peptide. Important roles played by water are discussed, and the alcohol effects on peptide conformations are newly analyzed.     

Density matrix and eigenstates for an excess electron in water

We extend the molecular theory of the solvated electrons [Chandler, Singh and Richardson, J. Chem. Phys. 81, 1975 (1984)] to calculate the density matrix for an excess electron in water. Using this density matrix, the numerically obtained solvent induced interaction [Miura and Hirata, J. Phys. Chem. 98, 9649 (1994)] and our developed method [Sethia, Sanyal and Singh, J. Chem. Phys. 93, 7268 (1990)], we have calculated the eigenstates of the electron in water. These results show that the excees electron in water behaves almost like a free particle with effective mass m* in a constant potential well.     

Substituent effect on the cationic ring‐opening polymerization of acyloxymethyl five‐member cyclic dithiocarbonates

Five‐member cyclic dithiocarbonates were synthesized by the reactions of carbon disulfide with benzoic, p‐anisic, p‐chlorobenzoic, 1‐naphthalenecarboxylic, p‐nitrobenzoic, and p‐(tert‐butyl)benzoic glycidyl esters, and their cationic ring‐opening polymerizations were carried out with methyl trifluoromethane sulfonate and trifluoromethane sulfonic acid as initiators at room temperature to 80 °C. Polymers with number‐average molecular weights of 3400–24,900 were obtained in high yields, and their structures were estimated by NMR and IR spectroscopy. The monomers showed a clear difference in the polymerization rate according to the substituents. The rate of polymerization decreased in the order of p‐chlorobenzoic ≥ benzoic > 1‐naphthalenecarboxylic > p‐nitro‐benzoic > p‐tert‐butylbenzoic > p‐anisic. The data of the reaction kinetics, NMR studies, and molecular orbital calculations proved a plausible mechanism involving the participation of p‐substituted benzoyloxymethyl groups to stabilize the cationic propagating end. The polymers showed decomposition temperatures with 5% weight loss ranging from 200 to 260 °C. No glass‐transition temperatures for the polymers were observed below 200 °C by differential scanning calorimetry. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3967–3980, 2001     

Equilibrium polymerization behavior in the cationic single ring‐opening polymerization of bicyclo orthoesters

The synthesis and cationic polymerization of the following bicyclo orthoesters were examined: 4‐ethyl‐2,6,7‐trioxabicyclo[2.2.2]octane, 1,4‐diethyl‐2,6,7‐trioxabicyclo[2.2.2]octane, 4‐ethyl‐1‐phenyl‐2,6,7‐trioxabicyclo[2.2.2]octane, 4‐ethyl‐1‐(4‐methoxyphenyl)‐2,6,7‐trioxabicyclo[2.2.2]octane, and 4‐ethyl‐1‐(4‐nitrophenyl)‐2,6,7‐ trioxabicyclo[2.2.2]octane. All the monomers underwent equilibrium polymerization, which was confirmed by the relationships between the polymerization temperature and monomer conversion. The obtained polymers afforded the original monomers via an acid‐catalyst treatment with a low reagent concentration in CH₂Cl₂ at 20 °C. The equilibrium monomer concentration was constant, regardless of the initial reagent concentration, in both polymerization and depolymerization. The bicyclo orthoesters with a bulky and electron‐withdrawing substituent showed a larger equilibrium monomer concentration. © 2001 John Wiley & Sons, Inc. J Polym Sci Part A: Polym Chem 39: 3159–3167, 2001     

Interpolation error estimates of a modified 8-node serendipity finite element

Summary. Interpolation error estimates for a modified 8-node serendipity finite element are derived in both regular and degenerate cases, the latter of which includes the case when the element is of triangular shape. For defined over a quadrilateral K, the error for the interpolant is estimated as , where in the regular case and in the degenerate case, respectively. Thus, the obtained error estimate in the degenerate case is of the same quality as in the regular case at least for . Results for some related elements are also given. Received June 2, 1997 / Published online March 16, 2000     

Polyacetylene and Polynorbornene Derivatives Carrying TEMPO. Synthesis and Properties as Organic Radical Battery Materials

Summary: 2,2,6,6‐Tetramethylpiperidine 1‐oxyl (TEMPO)‐containing N‐propargylamide HCCCH₂NHCO‐4‐TEMPO ( 1 ), propargyl ester HCCCH₂OCO‐4‐TEMPO ( 2 ), phenylacetylene derivative HCCC₆H₃‐3,4‐(CO₂‐4‐TEMPO)₂ ( 3 ), and norbornene diester monomers, NB‐2,3‐exo,exo‐(CH₂OCO‐4‐TEMPO)₂ ( 4 ), NB‐2,3‐endo,exo‐(COO‐4‐TEMPO)₂ ( 5a ), NB‐2,3‐endo,endo‐(COO‐4‐TEMPO)₂ ( 5b ) (NB = norbornene, TEMPO = 2,2,6,6‐tetramethyl‐1‐piperidinyloxyl) were synthesized and polymerized with rhodium and ruthenium catalysts. Monomers 2 , 5a , and 5b gave polymers with number‐average molecular weights of 47 000–185 000 in 59–100% yields, while 1 , 3 , and 4 gave polymers insoluble in common organic solvents in 88–100% yields. The capacities of cells fabricated with poly( 1 ), poly( 2 ), and poly( 3 ) were 67, 82, and 23 Ah · kg⁻¹ based on the weight, respectively. The capacity of poly( 5a )‐based cell reached the theoretical value (109 Ah · kg⁻¹) of the polymer.

Charge–discharge curves of poly( 5a ) at a current density of 0.13 mA · cm⁻² (100 mA · g⁻¹_{‐cathode active material}) in the voltage range of 2.5–4.2 V.     

Reaction of carbon dioxide with glycidol: The synthesis of a novel hyperbranched oligomer with a carbonate main chain with a hydroxyl terminal

A novel branched polycarbonate with a hydroxyl group at the chain end was synthesized by the copolymerization of glycidol with carbon dioxide (CO₂). The copolymerization was carried out with 5 mol % of an alkali metal halide or quaternary ammonium salt as a catalyst under atmospheric CO₂. The obtained poly(glycidol‐co‐carbon dioxide) was O‐benzoylated and O‐silylated, and the corresponding polymers were analyzed with IR, size exclusion chromatography, ¹³C NMR, and ²⁹Si NMR. The IR spectroscopy analysis of the O‐benzoylated polymer revealed that the maximum incorporation degree of the carbonate group was 90% (i.e., the CO₂/glycidol composition ratio was 0.9:1.0). The incorporation of CO₂ as a carbonate unit was also confirmed by the treatment of this polymer with n‐butylamine, which caused the aminolysis of the carbonate and led to degraded products. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2506–2511, 2004     

Role of cyclic dithiocarbonate as a promoter in the reaction of epoxide and imine in the presence of water

It was demonstrated that the reaction of epoxide and imine as a latent initiator under highly humid conditions was accelerated by addition of 5‐phenoxymethyl‐1,3‐oxathiolane‐2‐thione ( 1 ). When 1 was added to a mixture of glycidyl phenyl ether and an imine, the reaction of the epoxide with an amine released from the imine became faster than was the case without 1 , that is, 1 worked as a promoter of the reaction. The curing rate and initial adhesive strength of epoxy resin increased compared with that without 1 . © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4276–4283, 2004