Decomposition and Debromination of Monobromoacetic Acid by Radio Frequency Discharge in an Aqueous Solution

In this study, efficient decomposition and debromination of monobromoacetic acid (MBAA) induced by radio frequency discharge in an aqueous solution in the concentration range from 0.1 to 8.0 mM were investigated. The decomposition and debromination intermediate byproducts were analyzed by ion chromatography. The experimental results showed that the decay of MBAA followed first-order kinetics. Increasing pH and adding organic additives to the solution enhanced MBAA removal and debromination. Acetic acid, bromate ion, oxalic acid and formic acid were determined as the major intermediate byproducts. Final products were bromide ion and carbon dioxide. Hydrated electrons are the primary species for the debromination and reactive oxygen species are the ones for the decomposition. A probable reaction pathway was proposed. The present study may provide a promising alternative for the complete mineralization of MBAA.     

Addition of Surfactants and Non-Hydrolytic Proteins and Their Influence on Enzymatic Hydrolysis of Pretreated Sugarcane Bagasse

Poly(ethylene glycol) (PEG 4000) and bovine serum albumin (BSA) were investigated with the purpose of evaluating their influence on enzymatic hydrolysis of sugarcane bagasse. Effects of these supplements were assayed for different enzymatic cocktails (Trichoderma harzianum and Penicillium funiculosum) that acted on lignocellulosic material submitted to different pretreatment methods with varying solid (25 and 100 g/L) and protein (7.5 and 20 mg/g cellulose) loadings. The highest levels of glucose release were achieved using partially delignified cellulignin as substrate, along with the T. harzianum cocktail: increases of 14 and 18 % for 25 g/L solid loadings and of 33 and 43 % for 100 g/L solid loadings were reached for BSA and PEG supplementation, respectively. Addition of these supplements could maintain hydrolysis yield even for higher solid loadings, but for higher enzymatic cocktail protein loadings, increases in glucose release were not observed. Results indicate that synergism might occur among these additives and cellulase and xylanases. The use of these supplements, besides depending on factors such as pretreatment method of sugarcane bagasse, enzymatic cocktails composition, and solid and protein loadings, may not always lead to positive effects on the hydrolysis of lignocellulosic material, making it necessary further statistical studies, according to process conditions.     

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

\(\alpha\)-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.     

Comparing pharmacophore models derived from crystallography and NMR ensembles

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225–8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the “extra” pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.     

Temperature effect on the optical properties of two different triphenylamine-based organic dyes

In this paper, we present the absorption and photoluminescence (PL) spectra of conjugated, metal-free organic dyes, triphenylamine derivatives 3-(4-(bis(4-(5-(4-(hexyloxy)phenyl)thiophenyl)phenyl)amino)phenyl)-2-cyanoacrylic acid (OD3) and (E)-3-(5′-(4-(bis(4-(5-(4-hexyloxy)phenyl)thiophen-2-yl)phenyl)amino)phenyl)-2,2′-bithiophen-5-yl)-2-cyanoacrylic acid (OD3DT), with and without a π-conjugated bridge, respectively, in film at a temperature range from 13 to 400 K. We find that the intensities of absorption and PL of OD3 decrease gradually beyond 200 K, as well as the ratios of integral areas of absorption to PL spectra. However, the other compound, OD3DT, shows a very different behavior. An increase is discovered in the ratio of the absorption to PL integral area when the temperature is higher than 200 K. A π-conjugated bridge gives this compound a higher degree of symmetry, and therefore, a better alignment of the molecules in the film, which causes a stacking aggregation such that the temperature effect on this compound is different than OD3.     

Molden 2.0: quantum chemistry meets proteins

Since the first distribution of Molden in 1995 and the publication of the first article about this software in 2000 work on Molden has continued relentlessly. A few of the many improved or fully novel features such as improved and broadened support for quantum chemistry calculations, preparation of ligands for use in drug design related softwares, and working with proteins for the purpose of ligand docking.     

Facile synthesis of novel [1,3]oxazino[2,3-c][1,2,4] thiadiazin-12-one derivatives

Several novel fused heterocyclic systems which have rings containing N/O or N/S have been synthesized through a facile one-pot method by the treatment of substituted 2-(benzo[d]thiazol-2-yl)phenol and cyanogen bromide in THF and NEt₃. This one-pot method contains tough ring-opening of thiazole, special intermolecular rearrangement and ring-closing reactions. The newly synthesized compounds were characterized by HR-MS, ¹H-NMR, ¹³C-NMR spectral data and DFT calculation analysis. 2a was also determined by X-ray crystallographic analysis.     

An efficient synthesis of 3,4-dihydropyrimidin-2(1<Emphasis Type="Italic">H</Emphasis>)-one and 5,6-diphenylpyrimidine derivatives under solvent-free and base conditions

An efficient and convenient Biginelli-like reaction one-pot synthesis of a series of 4-aryl-5,6-diphenyl-3,4-dihydropyrimidin-2(1H)-one and 4-aryl-5,6-diphenylpyrimidine derivatives under solvent-free conditions from the reaction of aromatic aldehydes, 1,2-diphenylethanone, urea, guanidine carbonate or acetamidine hydrochloride has been reported. This methodology has the advantages of short reaction time, mild reaction conditions, easy work-up and environmental friendliness. Moreover, 4-aryl-5,6-diphenylpyrimidine derivatives were first reported in this process. The structures of the title compounds were further determined by X-ray diffraction. More importantly, different from general Biginelli reaction, this reported method was carried out under base conditions.     

Cholinesulfuric acid ionic liquid catalyzed an eco-friendly synthesis of 2,3-dihydroquinazolin-4(1H)-one in aqueous media

An efficient and straightforward approach to the synthesis of 2,3-dihydroquinazolin-4(1H)-one from 2-aminobenzamide and carbonyl compounds (aldehydes and ketones) using biocompatible choline sulfate-based acidic ionic liquid as a cheap and readily available catalyst in water has been developed. Various 2,3-dihydroquinazolin-4(1H)-one have been prepared using low-cost and environmental friendly solvent and catalyst in good to excellent yields in a shorter reaction time. The choline sulfate catalyst was prepared using a simple method from readily available starting material and was confirmed by ¹H NMR, FTIR, and TGA. The ease of the product separation without organic solvent and column chromatography and the reusability of the acidic ionic liquid catalyst makes this method economically affordable for large-scale synthesis.