Development of models for prediction of the antioxidant activity of derivatives of natural compounds

Antioxidants are important for maintaining the appropriate balance between oxidizing and reducing species in the body and thus preventing oxidative stress. Many natural compounds are being screened for their possible antioxidant activity. It was found that a mushroom pigment Norbadione A, which is a pulvinic acid derivative, shows an antioxidant activity; the same was found for other pulvinic acid derivatives and structurally related coumarines. Based on the results of in vitro studies performed on these compounds as a part of this study quantitative structure–activity relationship (QSAR) predictive models were constructed using multiple linear regression, counter-propagation artificial neural networks and support vector regression (SVR). The models have been developed in accordance with current QSAR guidelines, including the assessment of the models applicability domains. A new approach for the graphical evaluation of the applicability domain for SVR models is suggested. The developed models show sufficient predictive abilities for the screening of virtual libraries for new potential antioxidants.     

Synthesis and Catalytic Use of Gold(I) Complexes Containing a Hemilabile Phosphanylferrocene Nitrile Donor

Removal of the chloride ligand from [AuCl( 1 ‐κP)] ( 2 ) containing a P‐monodentate 1′‐(diphenylphosphanyl)‐1‐cyanoferrocene ligand ( 1 ), by using silver(I) salts affords cationic complexes of the type [Au( 1 )]X, which exist either as cyclic dimers [Au( 1 )]₂X₂ ( 3 a , X=SbF₆; 3 c , X=NTf₂) or linear coordination polymers [Au( 1 )]_nX_n ( 3 a′ , X=SbF₆; 3 b′ , X=ClO₄), depending on anion X and the isolation procedure. As demonstrated for 3 a′ , the polymers can be readily cleaved by the addition of donors, such as Cl^?, tetrahydrothiophene (tht) or 1 , giving rise to the parent compound 2 , [Au(tht)( 1 ‐κP)][SbF₆] ( 5 a ) or [Au( 1 ‐κP)₂][SbF₆] ( 4 a ), respectively, of which the last two compounds can also be prepared by stepwise replacement of tht in [Au( 1 ‐κP)₂][SbF₆]. The particular combination of a firmly coordinated (phosphane) and a dissociable (nitrile) donor moieties renders complexes 3/3′ attractive for catalysis because they can serve as shelf‐stable precursors of coordinatively unsaturated Au^I fragments, analogous to those that result from the widely used [Au(PR₃)(RCN)]X catalysts. The catalytic properties of the Au‐ 1 complexes were evaluated in model annulation reactions, such as the synthesis of 2,3‐dimethylfuran from (Z)‐3‐methylpent‐2‐en‐4‐yn‐1‐ol and oxidative cyclisation of alkynes with nitriles to produce 2,5‐disubstituted 1,3‐oxazoles. Of the compounds tested ( 2 , 3 a′ , 3 b′ , 3 a , 4 a and 5 a ), the best results were consistently achieved with dimer 3 c , which has good solubility in organic solvents and only one firmly bound donor at the gold atom. This compound was advantageously used in the key steps of annuloline and rosefuran syntheses.     

Sustainable Synthesis of Chiral Tetrahydrofurans through the Selective Dehydration of Pentoses

L ‐Arabinose is an abundant resource available as a waste product of the sugar beet industry. Through use of a hydrazone‐based strategy, L ‐arabinose was selectively dehydrated to form a chiral tetrahydrofuran on a multi‐gram scale without the need for protecting groups. This approach was extended to other biomass‐derived reducing sugars and the mechanism of the key cyclization investigated. This methodology was applied to the synthesis of a range of functionalized chiral tetrahydrofurans, as well as a formal synthesis of 3R‐3‐hydroxymuscarine.     

π‐Expanded α,β‐Unsaturated Ketones: Synthesis,Optical Properties,and Two‐Photon‐Induced Polymerization

A library of π‐expanded α,β‐unsaturated ketones was designed and synthesized. They were prepared by a combination of Wittig reaction, Sonogashira reaction, and aldol condensation. It was further demonstrated that the double aldol condensation can be performed effectively for highly polarized styrene‐ and diphenylacetylene‐derived aldehydes. The strategic placement of two dialkylamino groups at the periphery of D ‐π‐A‐π‐D molecules resulted in dyes with excellent solubility. These ketones absorb light in the region 400–550 nm. Many of them display strong solvatochromism so that the emission ranges from 530–580 nm in toluene to the near‐IR region in benzonitrile. Ketones based on cyclobutanone as central moieties display very high fluorescence quantum yields in nonpolar solvents, which decrease drastically in polar media. Photophysical studies of these new functional dyes revealed that they possess an enhanced two‐photon absorption cross section when compared with simpler ketone derivatives. Due to strong polarization of the resulting dyes, values of two‐photon absorption cross sections on the level of 200–300 GM at 800 nm were achieved, and thanks to that as well as the presence of the keto group, these new two‐photon initiators display excellent performance so that the operating region is 5–75 mW in some cases.     

Nature of the water/aromatic parallel alignment interactions

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O? H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE_{CCSD(T)(limit)} = ?2.45 kcal mol^?1 at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry‐adapted perturbation theory, and extended transition state‐natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV‐based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O? H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.     

MOLSIM: A modular molecular simulation software

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Synthesis of Heterocyclic Analogs of α‐aminoadipic Acid and its Esters Based on Imidazo[2,1‐b][1,3]Thiazole

A method for the preparation of heterocyclic analogs of α‐aminoadipic acid and its esters based on the imidazo[2,1‐b][1,3]thiazole ring system was developed. In this method, free‐radical bromination of ethyl 6‐methylimidazo[2,1‐b][1,3]thiazole‐5‐carboxylate with NBS afforded a versatile building block, ethyl 6‐bromomethylimidazo[2,1‐b][1,3]thiazole‐5‐carboxylate. Coupling of ethyl 6‐bromomethylimidazo[2,1‐b][1,3]thiazole‐5‐carboxylate with Schöllkopf's chiral auxiliary followed by acidic hydrolysis generated ethyl 6‐[(2S)‐2‐amino‐3‐methoxy‐3‐oxopropyl]imidazo[2,1‐b][1,3]thiazole‐5‐carboxylate. A similar procedure using diethyl (Boc‐amino)malonate yielded racemic 2‐amino‐3‐[(5‐ethoxycarbonyl)imidazo[2,1‐b][1,3]thiazol‐6‐yl]propanoic acid.     

The Identification of a Novel Highly Condensed Pentacyclic Heteroaromatic Ring System 1,3,5,5b,6,8,10,10b‐Octaazacyclopenta[h,i]Aceanthrylene and its Application in the Synthesis of 5,7‐Substituted Pyrazolo[4,3‐d]Pyrimidines

Pyrazolo[4,3‐d]pyrimidines are of interest as potential kinase inhibitors. This article describes the formation of a novel highly conjugated, condensed, centrosymmetric heteroaromatic compound, 4,9‐dichloro‐2,7‐diisopropyl‐1,3,5,5b,6,8,10,10b‐octaazacyclopenta[h,i]aceanthrylene ( 3 ), during the chlorination of 5,7‐dihydroxypyrazolo[4,3‐d]pyrimidine ( 1 ) with phenylphosphonic dichloride. The nucleophilic attack of benzylamine on 3 afforded N‐benzyl‐5‐chloro‐3‐isopropyl‐1H‐pyrazolo[4,3‐d]pyrimidin‐7‐amine ( 6 ), which was further substituted to yield a pyrazolo[4,3‐d]pyrimidine analogue of roscovitine, a well‐known cyclin‐dependent kinase inhibitor.     

High‐throughput workflow for identification of phosphorylated peptides by LC‐MALDI‐TOF/TOF‐MS coupled to in situ enrichment on MALDI plates functionalized by ion landing

We report an MS‐based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high‐throughput sample analysis. The workflow is based on an in situ enrichment on matrix‐assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO₂ using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO₂ into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high‐performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn‐based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal‐to‐noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12‐myristate 13‐acetate. These phosphorylations concerned the mitogen‐activated protein kinase/extracellular signal‐regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non‐activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high‐performance liquid chromatography gradient. Copyright © 2015 John Wiley & Sons, Ltd.