Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers

We apply several methods to probe the ensemble kinetic and structural properties of a model system of poly-phenylacetylene (pPA) oligomer folding trajectories. The kinetic methods employed included a brute force accounting of conformations, a Markovian state matrix method, and a nonlinear least squares fit to a minimalist kinetic model used to extract the folding time. Each method gave similar measures for the folding time of the 12-mer chain, calculated to be on the order of 7 ns for the complete folding of the chain from an extended conformation. Utilizing both a linear and a nonlinear scaling relationship between the viscosity and the folding time to correct for a low simulation viscosity, we obtain an upper and a lower bound for the approximate folding time within the range 70 ns相似文献   

Synthesis of monodisperse polymers from proteins

Proteins are functional biopolymers; viewed as molecules, they are also monodisperse polyamides with chemically reactive side chains. This paper describes the use of proteins as starting materials for the synthesis of monodisperse polymers with nonbiological functionalities attached to the side chains. It demonstrates the complete derivatization of amine groups (lysine side chains and N-termini) on three different proteins by addition of activated carboxylate reagents in aqueous solutions containing sodium dedecyl sulfate (SDS), under denaturing conditions. Several different acylating reagents were used to generate derivatized proteins; the resulting compounds constitute a new class of monodisperse, semisynthetic polymers, having the potential for wide variation in the structure of the backbone and of the side chains. Modification of lysozyme on a gram scale demonstrated that the method can generate useful quantities of material.     

Thermodynamic Parameters for the Association of Fluorinated Benzenesulfonamides with Bovine Carbonic Anhydrase II

This paper describes a calorimetric study of the association of a series of seven fluorinated benzenesulfonamide ligands (C₆H_nF_5?nSO₂NH₂) with bovine carbonic anhydrase II (BCA). Quantitative structure–activity relationships between the free energy, enthalpy, and entropy of binding and pK_a and log P of the ligands allowed the evaluation of the thermodynamic parameters in terms of the two independent effects of fluorination on the ligand: its electrostatic potential and its hydrophobicity. The parameters were partitioned to the three different structural interactions between the ligand and BCA: the Zn^II cofactor–sulfonamide bond (≈65 % of the free energy of binding), the hydrogen bonds between the ligand and BCA (≈10 %), and the contacts between the phenyl ring of the ligand and BCA (≈25 %). Calorimetry revealed that all of the ligands studied bind in a 1:1 stoichiometry with BCA; this result was confirmed by ¹⁹F NMR spectroscopy and X‐ray crystallography (for complexes with human carbonic anhydrase II).     

Proton‐bifurcated C—H⋯(O,O) hydrogen bonds in 2,3‐dichloro‐6‐nitro­benzyl­aminium chloride

In the crystal structure of the title salt, C₇H₇Cl₂N₂O₂⁺·Cl⁻, the chloride anions participate in extensive hydrogen bonding with the aminium cations and indirectly link the mol­ecules through multiple N⁺—H⋯Cl⁻ salt bridges. There are two independent mol­ecules in the asymmetric unit, related by a pseudo‐inversion center. The direct inter­molecular coupling is established by C—H⋯O, C—H⋯Cl and C—Cl⋯Cl⁻ inter­actions. A rare three‐center (donor bifurcated) C—H⋯(O,O) hydrogen bond is observed between the methyl­ene and nitro groups, with a side‐on intra­molecular component of closed‐ring type and a head‐on inter­molecular component.     

Development and validation of LC‐MS/MS method for the estimation of β‐hydroxy‐β‐methylbutyrate in rat plasma and its application to pharmacokinetic studies

A simple, sensitive and specific high‐performance liquid chromatography mass spectrometry (LC‐MS/MS) method was developed and validated for the quantification of β‐hydroxy‐β‐methyl butyrate (HMB) in small volumes of rat plasma using warfarin as an internal standard (IS). The API‐4000 LC‐MS/MS was operated under the multiple reaction‐monitoring mode using the electrospray ionization technique. A simple liquid–liquid extraction process was used to extract HMB and IS from rat plasma. The total run time was 3 min and the elution of HMB and IS occurred at 1.48 and 1.75 min respectively; this was achieved with a mobile phase consisting of 0.1% formic acid in a water–acetonitrile mixture (15:85, v/v) at a flow rate of 1.0 mL/min on a Agilent Eclipse XDB C₈ (150 × 4.6, 5 µm) column. The developed method was validated in rat plasma with a lower limit of quantitation of 30.0 ng/mL for HMB. A linear response function was established for the range of concentrations 30–4600 ng/mL (r > 0.998) for HMB. The intra‐ and inter‐day precision values for HMB were acceptable as per Food and Drug Administration guidelines. HMB was stable in the battery of stability studies, viz. bench‐top, autosampler freeze–thaw cycles and long‐term stability for 30 days in plasma. The developed assay method was applied to a bioavailability study in rats. Copyright © 2012 John Wiley & Sons, Ltd.     

Convergence of Szász-Beta operators

In the present article we find the hypergeometric representation of the Szász-Beta operators and obtain the moments using confluent hypergeometric functions, which can be related to generalized Laguerre polynomials. Then we estimate a convergence result for functions having bounded derivatives.     

A Novel Synthesis of 5-Aryltropoxe Derivatives

The reaction of substituted arylboronic acids with 5-bromo-2-methoxytropone catalyzed by palladium(0) complex furnished 5-arylated tropone derivatives in good yield.     

Approximation by complex szász-durrmeyer operators in compact disks

In the present paper, we deal with the complex Szász-Durrmeyer operators and study Voronovskaja type results with quantitative estimates for these operators attached to analytic functions of exponential growth on compact disks. Also, the exact order of approximation is found.     

Thermal comparison and multi-objective optimization of single-stage aqua-ammonia absorption cooling system powered by different solar collectors

Journal of Thermal Analysis and Calorimetry - This paper presents the comprehensive thermodynamic modelling to compare the performance and optimization of single-stage NH3–H2O-type absorption...