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Abstract: Monte Carlo simulations based on rotational isomeric state models were carried out to determine how amorphous polyethylene chains are deformed by the presence of spherical filler particles. The resulting distributions of the chain end-to-end distances were then employed to calculate mechanical properties of the cross-linked chains. The basic goals were (i) to refine previous simulations of this type carried out on this system to remove possible sampling biases, and (ii) to document the circumstances under which the particles stretch the chains to larger end-to-end distances, rather than compress them to smaller distances, and (iii) to study in more detail the flattening of the chains near particle surfaces. Comparisons with experiments include filler-induced changes in chain dimensions measured by neutron scattering, and general features of the stress–strain isotherms widely observed for reinforced elastomers in simple elongation. [Copyright &y& Elsevier]

Abstract: We derived the analytical solution of the eigenvalue problem for stereo-regular vinyl chains, such as stereo-regular polypropylene chains. The solution is applicable to all stereo-regular polymers of the type (AB) x which do not have symmetry between gauche + and gauche − states, and to polymers, such as polyoxymethylene or polydimethylsiloxane, for which symmetry between the gauche + and gauche − states does exist. For symmetric chains, the general solution of the eigenvalue problem is reduced to the known solution for polyoxymethylene chains. To illustrate the method the calculations have been performed for the three rotational states (trans, gauche + and gauche −) model, but the general algebraic solution is applicable for any ν rotational states models of polymer chains. We used the analytical solution of the eigenvalue problem to calculate numerically elastic properties of stereo-regular polypropylene chains within the framework of Mark–Curro theory (J Chem Phys, 79, 5705, 1983). [Copyright &y& Elsevier]

The transfer matrix method for generating lattice conformations of proteins is explained and applied to lattice proteins having high-level cooperativity to represent hydrophobic interactions. The main advantage of the method is the extremely efficient attrition-free generation and enumeration of compact conformations. We review the application of the method for the generation and complete, exact enumeration of all conformation for linear and cyclic chains in 2D on the square lattice and in 3D on the cubic lattice. We show for compact conformations that the growth of the chain in a piecewise way, cross-section by cross-section, is much more efficient than the traditional linear chain growth. We discuss an extension of the method by including information about the amino acid sequence. We develop a Zimm–Bragg [J Chem Phys 31 (1959) 476–85]-like theory of hydrophobic cluster formation by using the transfer matrix method. We show that the transfer matrix approach to the generation and averaging over chain conformations can be formulated as an algebraic problem. We show also how the transfer matrix method can be extended to off-lattice proteins. [Copyright &y& Elsevier]

The availability of many DNA-protein structures makes their classification timely and important. In this issue of Structure, the method of Akinori Sarai and his collaborators () utilizes aspects of the binding interactions and DNA properties to identify seven clusters of structures with a classification scheme that differs significantly from previous approaches. [Copyright &y& Elsevier]

Abstract: A new method for predicting protein secondary structure from amino acid sequence has been developed. The method is based on multiple sequence alignment of the query sequence with all other sequences with known structure from the protein data bank (PDB) by using BLAST. The fragments of the alignments belonging to proteins from the PBD are then used for further analysis. We have studied various schemes of assigning weights for matching segments and calculated normalized scores to predict one of the three secondary structures: α-helix, β-sheet, or coil. We applied several artificial intelligence techniques: decision trees (DT), neural networks (NN) and support vector machines (SVM) to improve the accuracy of predictions and found that SVM gave the best performance. Preliminary data show that combining the fragment mining approach with GOR V (Kloczkowski et al, Proteins 49 (2002) 154–166) for regions of low sequence similarity improves the prediction accuracy. [Copyright &y& Elsevier]

• An efficient one-pot synthesis of dihydropyrimidinones was performed with cysteine as a bio-organic catalyst. • These compounds (4a – 4j) displayed significant in vitro urease inhibitory activity. • MTT assay was used to evaluate the cytotoxicity of all compounds in HT1080 human fibroblast cell lines. • The kinetic mechanism was investigated by Lineweaver-Burk plots. • In silico molecular docking studies supported the experimental results. The aim of the present research was to develop a one-pot, three-component method for the synthesis of some 3,4-dihydro pyrimidine-2-(1 H)-one (DHPM) derivatives using aldehydes, urea, and ethyl acetoacetate in the presence of cysteine as a green, bio-organic catalyst. This procedure has several key advantages, including a facile and convenient method, green and low-cost catalyst, high yield, short reaction time, and avoidance of the use of environmentally harmful solvents. It is important to note that the synthesized compounds (4a – j) were evaluated for in vitro urease inhibitory activity, and all were found to be more effective than the standard thiourea (IC 50 = 4.745 ± 0.054 µM), with urease inhibitory potentials between IC 50 = 0.058 ± 0.006 µM to 0.297 ± 0.066 µM. Lineweaver-Burk plots were used to study the kinetics of the most potent compound (4e), and the results showed that the compound non-competitively inhibited urease by forming an enzyme-inhibitor complex. In addition, HT1080 human fibroblast cell lines were used to test the toxicity of the synthesized compounds on cell viability using the MTT assay method, and all compounds except 4g, 4i, and 4j exhibited no significant toxic effects on cells even at high concentrations. Moreover, molecular docking was used to determine the binding interactions between the molecules (ligands) and the active site of the urease enzyme, and the ligands indicated acceptable binding energy values. [Display omitted] [ABSTRACT FROM AUTHOR]

[Display omitted] • A series of 1,3,4-thiadiazol-1,3,4-oxadiazol-acetamide derivatives (7a – 7j) were synthesized as elastase inhibitors. • The in-vitro elastase inhibitory activity of all synthesized compounds was determined successfully. • The kinetic mechanism was investigated by Lineweaver-Burk plots. • MTT assay was used to evaluate the cytotoxicity of all compounds on B16F10 melanoma cell lines. • Molecular docking was applied to investigate the binding affinity of compounds with elastase and the ligands showed good binding energy values. Considering the biological significance of 1,3,4-thiadiazole/oxadiazole heterocyclic scaffolds, a novel series of 1,3,4-thiadiazole-1,3,4-oxadiazole-acetamide derivatives (7a – j) was designed and synthesized using molecular hybridization. The inhibitory effects of the target compounds on elastase were evaluated, and all of these molecules were found to be potent inhibitors compared to the standard reference oleanolic acid. Compound 7f exhibited the excellent inhibitory activity (IC 50 = 0.06 ± 0.02 μM), which is 214-fold more active than oleanolic acid (IC 50 = 12.84 ± 0.45 μM). Kinetic analysis was also performed on the most potent compound (7f) to determine the mode of binding with the target enzyme, and it was discovered that 7f inhibits the enzyme in a competitive manner. Furthermore, the MTT assay method was used to assess their toxicity on the viability of B16F10 melanoma cell lines, and all compounds did not display any toxic effect on the cells even at high concentrations. The molecular docking studies of all compounds also justified with their good docking score and among them, compound 7f had a good conformational state with hydrogen bond interactions within the receptor binding pocket, which is consistent with the experimental inhibition studies. [ABSTRACT FROM AUTHOR]

Abstract: This review illustrates how elastomer reinforcement can be modeled using Monte Carlo simulations on rotational isomeric state chains to characterize their spatial configurations in the vicinity of filler particles. The results are distributions of the chain end-to-end distances as perturbed by this excluded-volume effect, and the results obtained are in agreement with experimental results gotten by neutron scattering. The use of these distributions in standard molecular theories of rubberlike elasticity then produces stress–strain isotherms suitable for comparison with those in elongation experiments. Such simulations have now been carried out for elastomeric matrices reinforced by spherical filler particles (either on a cubic lattice or randomly dispersed), or by prolate or oblate particles on cubic lattices (either with their axes oriented or randomized). The simulated mechanical properties are consistent with experimental results available at the present time, and should provide encouragement and guidance for additional simulations and experiments. [Copyright &y& Elsevier]

Abstract: The elastomeric properties of networks of stereoregular polypropylenes (PP) filled with spherical nanoparticles have been modeled in an attempt to obtain better insights into elastomer reinforcement. The polymers were either isotactic or syndiotactic PP in the amorphous state, and the simulations were based on rotational isomeric state (RIS) theory combined with the largest eigenvalue method for deriving conditional bond probabilities. Monte Carlo simulations gave distributions of the end-to-end distance of these chains in the presence of the particles, and these were used in the Mark–Curro theoretical approach to calculate values of the normalized stress, and the reduced stress (shear modulus) under uniaxial stretching. The simulations were calculated for PP chains having 100–200 skeletal bonds, for several temperatures from 481 to 650K, and for varying filler particle sizes (up to 100Å). The presence of the filler nanoparticles was found to influence chain conformations, frequently leading to significant chain extensions, which significantly affect the elastomeric properties of the nanocomposites. [Copyright &y& Elsevier]