On the computational aspects of Rosenbrock procedures with built-in error estimates for stiff systems

A third orderA-stable Rosenbrock method with built-in error estimate is developed by modifying an idea of J. R. Cash. Comparative tests are presented.     

Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models

Implicit solvent models for biomolecular simulations have been developed to use in place of more expensive explicit models; however, these models make many assumptions and approximations that are likely to affect accuracy. Here, the changes in free energies of solvation upon folding of several fast folding proteins are calculated from previously run μs–ms simulations with a number of implicit solvent models and compared to the values needed to be consistent with the explicit solvent model used in the simulations. In the majority of cases, there is a significant and substantial difference between the values calculated from the two approaches that is robust to the details of the calculations. These differences could only be remedied by selecting values for the model parameters—the internal dielectric constant for the polar term and the surface tension coefficient for the nonpolar term—that were system‐specific or physically unrealistic. We discuss the potential implications of our findings for both implicit and explicit solvent simulations. © 2015 Wiley Periodicals, Inc.     

Electrochemical sensing of bisphenol A on single-walled carbon nanotube paper electrodes

The electrochemical detection of BPA often requires modification of electrodes to overcome BPA′s slower kinetics and higher oxidation potential. This work reports a modification-free, paper electrode based on vacuum-filtered SWCNT thin film. The prepared electrode does not need to be polished or transferred into the conducting substrates. The linear sweep voltammetric detection showed a linear response from 0.5–10 μM and 25–100 μM with the experimental LOD of 1.0 μM (S/N=3). The interference study and good recovery percentage (93–105 %) in real water samples demonstrated the method‘s selectivity. The sensor can be promising for developing a simple, low-cost, portable, and paper-based BPA monitoring system.     

Synthetic Peptide Antibodies as TNF-α Inhibitors: Molecularly Imprinted Polymer Nanogels Neutralize the Inflammatory Activity of TNF-α in THP-1 Derived Macrophages

Tumor Necrosis Factor-α (TNF-α) is a cytokine that is normally produced by immune cells when fighting an infection. But, when too much TNF-α is produced as in autoimmune diseases, this leads to unwanted and persistent inflammation. Anti-TNF-α monoclonal antibodies have revolutionized the therapy of these disorders by blocking TNF-α and preventing its binding to TNF-α receptors, thus suppressing the inflammation. Herein, we propose an alternative in the form of molecularly imprinted polymer nanogels (MIP-NGs). MIP-NGs are synthetic antibodies obtained by nanomoulding the 3-dimensional shape and chemical functionalities of a desired target in a synthetic polymer. Using an in-house developed in silico rational approach, epitope peptides of TNF-α were generated and ‘synthetic peptide antibodies’ were prepared. The resultant MIP-NGs bind the template peptide and recombinant TNF-α with high affinity and selectivity, and can block the binding of TNF-α to its receptor. Consequently they were applied to neutralize pro-inflammatory TNF-α in the supernatant of human THP-1 macrophages, leading to a downregulation of the secretion of pro-inflammatory cytokines. Our results suggest that MIP-NGs, which are thermally and biochemically more stable and easier to manufacture than antibodies, and cost-effective, are very promising as next generation TNF-α inhibitors for the treatment of inflammatory diseases.     

A computational study of lithium ketone enolate aggregation in the gas phase and in THF solution

The aggregation state of several lithium enolates were calculated in the gas phase and in THF solution by the B3LYP DFT and MP2 methods. The gas phase free energies of aggregate formation were underestimated by the DFT calculations, compared to those obtained by the G3MP2 method, although DFT did correctly predict the hexamer to be the major gas phase species. The DFT calculations correctly predicted the tetramer to be the major species in THF, while MP2 underestimated the stability of the tetramer relative to the dimer.     

Weighted Norm Inequalities for Spectral Multipliers on Graphs

Let Γ be a graph endowed with a reversible Markov kernel p, whose associated operator P is defined by \(Pf(x) = {\sum }_{y} p(x, y)f(y)\). We assume that the kernels p_n(x, y) associated to Pⁿ satisfy Gaussian upper bounds but do not assume they satisfy the Hölder continuity property and the temporal regularity. Denote by L = I ? P the discrete Laplacian on Γ. This article shows the weighted weak type (1, 1) estimates and the weighted L^p norm inequalities for the spectral multipliers of L. We also obtain the weighted L^p norm inequalities for the commutators of the spectral multipliers of L with BMO functions which are new even for the unweighted case.     

Plastic Antibodies for Cosmetics: Molecularly Imprinted Polymers Scavenge Precursors of Malodors

Molecularly imprinted polymers (MIPs) are synthetic antibody mimics capable of specific molecular recognition. Advantageously, they are more stable, easy to tailor for a given application and less expensive than antibodies. These plastic antibodies are raising increasing interest and one relatively unexplored domain in which they could outplay these advantages particularly well is cosmetics. Here, we present the use of a MIP as an active ingredient of a cosmetic product, for suppressing body odors. In a dermo‐cosmetic formulation, the MIP captures selectively the precursors of malodorous compounds, amidst a multitude of other molecules present in human sweat. These results pave the way to the fabrication of a novel generation of MIPs with improved selectivities in highly complex aqueous environments, and should be applicable to biotechnological and biomedical areas as well.     

Iron-sulfur proteins as initiators of radical chemistry

Iron-sulfur proteins are very versatile biological entities for which many new functions are continuously being unravelled. This review focus on their role in the initiation of radical chemistry, with special emphasis on radical-SAM enzymes, since several members of the family catalyse key steps in the biosynthetic pathways of cofactors such as biotin, lipoate, thiamine, heme and the molybdenum cofactor. It will also include other examples to show the chemical logic which is emerging from the presently available data on this family of enzymes. The common step in all the (quite different) reactions described here is the monoelectronic reductive cleavage of SAM by a reduced [4Fe-4S](1+) cluster, producing methionine and a highly oxidising deoxyadenosyl radical, which can initiate chemically difficult reactions. This set of enzymes, which represent a means to perform oxidation under reductive conditions, are often present in anaerobic organisms. Some other, non-SAM-dependent, radical reactions obeying the same chemical logic are also covered.     

A molecular docking simulation study on potent inhibitors against Rhizoctonia solani and Magnaporthe oryzae in rice: silver-tetrylene and bis-silver-tetrylene complexes vs. validamycin and tricyclazole pesticides

Structural Chemistry - Rice, well known as the most important staple food source worldwide, is highly susceptible to many infectious diseases, especially rice sheath blight caused by fungus...